Operational Plan for the Restoration of Diadromous Fishes to the ...

Operational Plan for the Restoration of 

Diadromous Fishes to the Penobscot River 

Photo Courtesy of Randy Spencer 

Prepared By: 

Department of Marine Resources 

Department of Inland Fisheries and Wildlife 

For Presentation to the Atlantic Salmon Commission: 

Dick Ruhlin, Chair, Member-at-large 

George Lapointe, Commissioner of the Department of Marine Resources 

R. Dan Martin, Commissioner of the Department of Inland Fisheries and Wildlife 

Editor: 

Melissa Laser, Department of Marine Resources 

Approved July 2, 2009

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Table of Contents 

Introduction ................................................................................................................ 1 

Section 1 - Alewife, American eel, American shad, Atlantic salmon, Atlantic 

sturgeon, Atlantic tomcod, blueback herring, rainbow smelt, sea lamprey, sea-run 

brook trout, shortnose sturgeon, and striped bass..................................................... 3 

Background ............................................................................................................ 4 

Introduction ............................................................................................................ 5 

Operational Objectives, Measures, and Strategies ................................................ 6 

Work Plan Table................................................................................................... 15 

Work Plan Narratives ........................................................................................... 16 

References........................................................................................................... 27 

Atlantic Salmon .................................................................................................... 28 

Introduction .......................................................................................................... 28 

Background .......................................................................................................... 28 

Strategies to Increase Adult Escapement to the Penobscot Basin....................... 30 

Operational Objectives ......................................................................................... 30 

Operational Measures .......................................................................................... 31 



References........................................................................................................... 46 

Section 2 - Passage and Connectivity ..................................................................... 47 

Introduction .......................................................................................................... 48 

Goal, Objectives, and Strategies.......................................................................... 54 



References........................................................................................................... 81 

Section 3 - Habitat ................................................................................................... 83 

Introduction .......................................................................................................... 84 

Background .......................................................................................................... 84 

Goals, Objectives and Strategies ......................................................................... 85 



References........................................................................................................... 91 

Section 4 - Non-Native species including Northern pike .......................................... 93 

Introduction .......................................................................................................... 94 

Goal, Objectives and Strategies........................................................................... 94 



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Section 5 - Analyze, Synthesize, and Communicate Results to Inform Future 

Adaptive Management Actions, Analyses, and Research...................................... 102 

Introduction ........................................................................................................ 103 

Goal, Objectives and Strategies......................................................................... 103 

Work Plan Table................................................................................................. 106 

Work Plan Narratives ......................................................................................... 109 

Appendices ............................................................................................................ 115 

Appendix A - Role of Hatchery Releases or Exogenous Stock Transfers in Alosine 

Restoration ............................................................................................................ 116 

Appendix B - Viability of Salmon Sub-Populations by Reach in the Penobscot Basin 

............................................................................................................................... 130 

Appendix C - Penobscot Habitat and Freshwater Juvenile Atlantic Salmon 

Production Potential............................................................................................... 141 

Appendix D - Adaptive Management Guidance for Fisheries Management in the 

Penobscot Basin.................................................................................................... 162 

Appendix E - Atlantic Salmon Fisheries Management Options and Strategies...... 171 

Appendix F - Atlantic Salmon Strategic Objectives................................................ 178 

Appendix G - Habitat Survey and Assessment Plan for the Penobscot Basin....... 187 

Appendix H - Developing a Sampling Plan for the Penobscot Basin ..................... 190 

Penobscot Watershed Survey Design ................................................................... 195 

Appendix I – Downstream Passage Studies for Atlantic Salmon ........................... 199 

Appendix J – Northern Pike Risk Assessment for Piscataquis River ..................... 206 

Appendix K – Northern Pike Movement Barrier Risk Assessment Survey............. 300 

Addendum - Response to Comments and Suggested changes to the Draft 

Operational Plan for the Restoration of Diadromous Fishes to the Penobscot River 

7-2-09……………………………………………………………………………………...330 

Addendum - Memorandum of Understanding Penobscot River Invasive Species and 

Barrier Agreement: A Joint Agreement Between the Maine Department of Inland 

Fisheries and Wildlife and the Maine Department of Marine 

Resources………………………………………………………………………………...354 

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Introduction 

The overarching goal of the Operational Plan is to restore and guide management of 

diadromous fish populations, aquatic resources, and the ecosystems on which they 

depend, for their intrinsic, ecological, economic, recreational, scientific, and 

educational values for use by the public. The state fisheries agencies, the Maine 

Department of Marine Resources (MDMR) and the Maine Department of Inland 

Fisheries and Wildlife (MDIFW) are committed to working together and in 

cooperation with the Penobscot Indian Nation (PIN), the U.S. Fish and Wildlife 

Service (USFWS), and National Oceanic and Atmospheric Administration’s National 

Marine Fisheries Service (NOAA Fisheries), in this effort. There are also many 

stakeholders with an interest in the watershed that have led and continue to lead 

restoration efforts. Various non-governmental organizations (NGOs) have worked to 

restore diadromous fish populations by succeeding with removal of a hydropower 

dam in Souadabscook Stream, the removal of the Brownville Dam, and active efforts 

to improve fish passage in Blackman Stream, Great Works Stream, and 

Sedgeunkedunk Stream. Researchers from the University of Maine (UM) and other 

institutions have worked cooperatively with state and federal agencies, providing 

detailed information on multiple fish species and the environment throughout the 

basin. The Penobscot River Restoration Trust (PRRT or Trust) has worked tirelessly 

on the Penobscot River Restoration Project (PRRP). 

The Operational Plan is intended to complement the PRRP, which was made 

possible by the Lower Penobscot River Multiparty Settlement Agreement signed in 

June 2004 by PPL Corporation (PPL), state and federal resource agencies, the PIN, 

and various NGOs 1 . This unprecedented and historic agreement provides the 

PRRT, a non-profit organization, the option to purchase three dams from PPL, 

decommission and remove the two lowermost dams on the main stem of the river 

(Veazie and Great Works), and decommission and pursue construction of an 

innovative experimental fish bypass around the Howland Dam, located upstream on 

the Piscataquis River. 

MDMR and MDIFW completed a Strategic Plan for the Restoration of Diadromous 

Fishes to the Penobscot River (SMP) in 2007 2 . The plan was reviewed by the PIN, 

NOAA, USFWS, and other interested parties. The plan defined four strategic goals: 

(1) coordinating fisheries management activities into a cohesive multispecies 

management program, (2) providing safe, timely, and effective fish passage 

(upstream and downstream), (3) maintaining or improving habitat for diadromous 

and select resident species, and (4) adopting an adaptive, ecosystem based 

management program. 

1 

American Rivers, Atlantic Salmon Federation, Maine Audubon, Natural Resources Council of Maine, 

The Nature Conservancy, and Trout Unlimited 

2 

Available online at http://www.maine.gov/dmr/searunfish/reports/PenobscotPlanMarch2008.pdf 

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The operational plan details actions to accomplish the strategic plan objectives, 

incorporates multi-species management, and will be revised as needed in 

conjunction with barrier removals and improved access to habitat. There is an 

urgency to begin restoration efforts for shad and river herring and to increase efforts 

to restore Atlantic salmon; therefore some actions identified are currently underway. 

The 40 to 50-year time frame for the Strategic Plan, spanning 2010 through 2050- 

2060, has two stages. The first stage will be through the completion of the 

Penobscot River Restoration Project (approximately 2010-2014) and the second 

stage will be a 35 to 45-year period after the Project is complete (approximately 

2012-2032). 

This plan implements the long-term vision and is intended to provide guidance to 

MDMR and MDIFW on restoration actions for multiple species over the next 40-50 

years through the identification of shared goals, objectives, and strategies for 

restoration, recovery, and management of multiple fish species and ecosystem 

processes, using an adaptive management approach. The key ecosystem 

processes are hydrology, connectivity, and species assemblages. Understanding 

these processes are going to require collaborative efforts with researchers and other 

state and federal agencies. A primary responsibility of the interagency committee, 

as established under the Strategic Plan, will be to address interagency management 

issues in areas of overlapping jurisdiction. Members of the Interagency Technical 

Committee include, MDMR, MDIFW, PIN, NOAA, USFWS, and the Trust. MDMR 

and MDIFW will develop annual work plans based on the operational plan. 

The plan is divided into six sections. The first section represents species specific 

management information and is broken into two parts: 1) alewife, American eel, 

American shad, Atlantic sturgeon, Atlantic tomcod, blueback herring, rainbow smelt, 

sea lamprey, sea-run brook trout, shortnose sturgeon, and striped bass; and 2) 

Atlantic salmon. Section 2 discusses passage and connectivity issues for all species 

in the drainage. Section 3 addresses habitat issues for all species in the drainage. 

Issues pertaining to non-natives species are included in Section 4 with a risk 

assessment for Northern pike included in Appendix I. Section 5 focuses on 

mechanisms to integrate the various components including data management and 

analysis, through communication, analysis and plan synthesis. Finally, eleven 

appendices accompany the plan. 

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Section 1 - Alewife, American eel, American shad, Atlantic salmon, Atlantic 

sturgeon, Atlantic tomcod, blueback herring, rainbow smelt, sea lamprey, searun 

brook trout, shortnose sturgeon, and striped bass 

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Alewife, American eel, American shad, Atlantic sturgeon, Atlantic tomcod, 

blueback herring, rainbow smelt, sea lamprey, sea-run brook trout, shortnose 

sturgeon, and striped bass 

Author: Gail Wippelhauser 

Background 

As described in the Strategic Plan for the Restoration of Diadromous Fishes to the 

Penobscot River (“Strategic Plan” DMR DIFW 2008) the Penobscot River basin once 

supported large populations of diadromous fishes. The historical abundance of 

these fish will never be known with certainty, because populations had declined long 

before 1867 when Maine’s first Commissioners of Fisheries were appointed. 

Although information about historical abundance was scarce, the Commissioners 

described the historical range of commercially important species, and this 

information has been summarized in the Strategic Plan. Using information on the 

historical range of alewife and American shad and current data on habitat 

production, DMR developed an order-of-magnitude estimate of the number of adult 

alewife and shad that could return to the river each year. 3 

This Operational Plan proposes measures to restore native diadromous fishes to 

their historic habitat, to restore shad and alewife to their estimated historic 

abundance, and to significantly increase population abundances of the other 

diadromous species within a period of 40-50 years. The state of Maine proposes to 

restore diadromous fish populations on this aggressive schedule in order to minimize 

the risk of extirpation of extant populations due to random events (bycatch) or longterm 

environmental change (global warming), to provide ecological benefits to other 

species in the watershed including Atlantic salmon, and to provide fishing 

opportunities and a local source of food for people living in the watershed. 

This part of the operational plan outlines the prioritized objectives and tasks that will 

be undertaken to implement components of the Strategic Plan relevant to alewife 

(species-of-concern), American eel, American shad, Atlantic sturgeon (species-ofconcern), 

Atlantic tomcod, blueback herring (species-of-concern), rainbow smelt 

(species-of-concern), sea lamprey, sea-run brook trout, shortnose sturgeon 

(endangered species), and striped bass. There are no existing management actions 

for these species in the Penobscot, because of their general inability to migrate 

beyond the Veazie Dam (i.e., they cannot or will not use the existing upstream 

passage facility), and because of past funding and staffing constraints. 

3 The methodology for developing estimates is described in the Strategic Plan. 

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Introduction 

Five species (shortnose sturgeon, Atlantic sturgeon, rainbow smelt, Atlantic tomcod, 

and sea-run brook trout) likely did not migrate beyond the set of falls where Milford 

Dam is now located, and DMR assumes this site was their historical upstream limit 4 . 

With two exceptions, little is known about the current status of these species. In the 

1970s, DMR estimated the adult smelt population to be two million fish, comprised of 

at least five spawning stocks, and the annual catch to be 40,000-60,000 pounds 

(versus 266,875 or 366,875 pounds in 1887). Fernandez (2008) caught 25 Atlantic 

sturgeon and 151 shortnose sturgeon in the lower Penobscot (Veazie to Bucksport) 

between June 2006 and November 2007, and discovered a shortnose sturgeon 

overwintering area in Bangor near river km 36.5. His preliminary estimates of the 

river-wide shortnose sturgeon population were 1425 (95% CI: 203, 2647) and 

1531(95% CI: 885, 5681); no Atlantic sturgeon were recaptured, so a population 

estimate was not be made. 

Six species historically migrated varying distances beyond the falls at Milford 4 . The 

catadromous American eel was the most widely distributed, and traveled into the 

West Branch. Eels were commercially harvested in the 1990s as far upriver as 

Millinocket, and are still common in the watershed (Yoder 2005, NOAA 2008). 

Alewife, American shad, and presumably the closely related blueback herring 

reached the mouth of Wassataquoik Stream on the East Branch, Grand Falls or 

Shad Pond on the West Branch, and were found in all the major tributaries. 

Currently, a small number of alewife pass the Veazie Dam each year, American 

shad and blueback herring rarely do, and there is no evidence that these species 

regularly migrate beyond the Milford Dam (Yoder 2005, NOAA 2008; DIFW 

electrofishing databases). Remnant populations of American shad and blueback 

herring exist below the Veazie Dam (sizes unknown), and alewife runs occur in 

Souadabscook Stream (size unknown), and the Orland River. 

Although there is no information on their historical distribution, sea lamprey and 

striped bass probably migrated above Milford. Yoder (2005) and NOAA (2008) 

found sea lamprey below and above West Enfield. In some years, striped bass are 

often seen in the Veazie trap in substantial numbers, but there is no evidence that 

they historically spawned in the Penobscot River (as they did in the Kennebec) or 

that they currently do. 

Stocking is being proposed to restore alewife and American shad above Milford. 

Before making this decision, DMR considered the past success of stocking 

programs and existing genetic information on population differentiation (Appendix A). 

Four methods will be used to assess the restoration of alewife, American eel, 

American shad, blueback herring, sea lamprey, and striped bass: daily counts at fish 

4 Described in the Strategic Plan. 

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passages, weekly biological samples taken at Milford, biweekly beach seine 

surveys, and annual boat electrofishing survey. Additional special methods may be 

needed for the remaining species. 

Operational Objectives, Measures, and Strategies 

Throughout this section of the Operational Plan the first migration season after the 

removal of both Great Works Dam and Veazie Dam is termed Yr0. Further, selfsustaining 

is defined as “A population that exists in sufficient numbers to replace 

itself through time without supplementation (hatchery or wild caught fish or eggs).” 

1.0 Objective: Rebuild the shortnose sturgeon population to self-sustaining 

levels in historical habitat within 40 years. 

1.1 Measure: Beginning in Yr0 the shortnose sturgeon population will increase by 

30% 5 each generation (14 years) by natural reproduction of wild fish. 

1.1.1 Strategy: Estimate the size of the existing population by 2012 (or prior to Yr0). 

1.1.2 Strategy: Identify existing essential habitat by 2012 (or prior to Yr0). 

1.1.3 Strategy: Obtain genetic analysis by 2012 (or prior to Yr0). 

1.1.4 Strategy: Identify and quantify sources of mortality. 

1.1.5 Strategy: Estimate the size of the population at least 20 and 40 years after Yr0. 

1.1.6 Strategy: Reassess essential habitat 1-2, 20 and 40 years after Yr0. 

2.0 Objective: Rebuild the Atlantic sturgeon population to self-sustaining 


2.1 Measure: Beginning in Yr0 the Atlantic sturgeon population will increase by 30% 6 

each generation (20 years) by natural reproduction of wild fish. 

2.1.1 Strategy: Estimate the size of the existing population by 2012 (or prior to Yr0). 

2.1.2 Strategy: Identify existing essential habitat by 2012 (or prior to Yr0). 

2.1.3 Strategy: Obtain genetic analysis by 2012 (or prior to Yr0). 

2.1.4 Strategy: Identify and quantify sources of mortality. 

2.1.5 Strategy: Estimate the size of the population at least 20 and 40 years after Yr0. 

2.1.6 Strategy: Reassess essential habitat 1-2, 20 and 40 years after Yr0. 

5 Based on rate of increase in Kennebec River shortnose sturgeon determined from mark-recapture 

population estimates made in the late-1970s and mid-1990s. During this period there was significant 

improvement in water quality, but no change in available habitat. Ongoing telemetry studies indicate 

that shortnose sturgeon in the Penobscot River may be part of the Kennebec/Androscoggin 

population. 

6 CPUE data for Atlantic sturgeon in the Kennebec River increased by a factor of 10-25 over a 20year 

period from 1977 to 2000. However, the data are limited, and high flows in the early years may 

have caused low catches and low CPUE. In the absence of other data, we have assumed that 

Atlantic sturgeon will increase at the same rate as shortnose sturgeon. 

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3.0 Objective: Rebuild the rainbow smelt population to self-sustaining levels in 

historical habitat within 45 years. 

3.1 Measure: In Yr15 (5 generations or 15 years after Yr0) the rainbow smelt 

population will equal or exceed the 1970 level of abundance 7 or the current 

abundance, age structure will not have declined from the 1970 level or current level, 

and smelt will utilize the newly accessible habitat between Veazie and Milford. 

3.1.1 Strategy: Document the age structure of the existing rainbow smelt population 

by 2012 (or prior to Yr0). 

3.1.2 Strategy: Estimate the size of the rainbow smelt population in 2012 (or prior to 

Yr0) if feasible. 

3.1.3 Strategy: Estimate the size of the rainbow smelt population and assess its use 

of habitat between Veazie and Milford by Yr15. 

3.1.4 Strategy: Conduct biweekly beach seine survey to assess juvenile fishes. 

3.2 Measure: In Yr30 the rainbow smelt population will be 25% larger than in Yr15. 

3.2.1 Strategy: Estimate the size of the rainbow smelt population in Yr30. 

3.3 Measure: In Yr45 the rainbow smelt population will be 25% larger than in Yr30. 

3.3.1 Strategy: Estimate the size of the rainbow smelt population in Yr45. 

4.0 Objective: Rebuild the Atlantic tomcod population to self-sustaining levels 

in historical habitat within 40 years. 

4.1 Measure: Each five generations (15 years) after Yr0 the Atlantic tomcod 

population will increase by 10%, and mercury accumulation in body tissue will have 

decreased from 2008 levels. 

4.1.1 Strategy: Develop and institute a survey to assess trends in Atlantic tomcod 

population and habitat use. 

4.1.2 Strategy: Test tomcod periodically for mercury (see Habitat Section 3). 


5.0 Objective: Rebuild sea-run brook trout populations to self-sustaining 

levels in historic habitat within 40 years. 

5.1 Measure: The current distribution and abundance of brook trout populations with 

a sea-run component will remain stable or increase by Yr10 (10 years after Yr0). 

5.1.1. Identify brook trout populations in the Penobscot basin with a sea-run 

component by Yr5 (5 years after Yr0). 

7 DMR estimated the rainbow smelt population in the Penobscot River at two million fish, comprised 

of at least five spawning stocks[0]. 

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6.0 Objective: Restore alewife populations to self-sustaining levels in 

historical habitat within 40-48 years. 

6.1 Measure: Restore populations to 13 Phase 1 historical lakes (Table 1; Fig. 1) in 

16 years (four generations) or less beginning in 2010 or 2011. 

6.1.1 Strategy: Assess availability and sufficiency of in-basin or nearest out-of-basin 

sources of approximately 97,500 broodstock by 2010 or 2011. 

6.1.2 Strategy: Meet with lake associations prior to stocking new habitat. 

6.1.3 Strategy: Stock approximately six adult alewives per surface acre (97,500 

total) in Phase 1 lakes annually from 2010 (2011) to 2026 (2027) or until annual 

return rates to each lake are at least 35 adult per acre for four successive years, 

which equals annual adult returns at Milford of at least 532,000 fish. 

6.1.4 Strategy: Monitor adult alewife returns by annual counts at Milford, West 

Enfield, Pumpkin Hill, and Howland 8 , and conduct weekly biological sampling at 

Milford. 

6.1.5 Strategy: Assess and improve if needed upstream and downstream passage at 

barriers (see Passage and Connectivity 16.1, 17.0, 18.0 and Non-native species 

23.0 for timetables). 


6.1.7. Strategy: Conduct annual boat electrofishing survey to assess changes in 

community structure. 

6.2 Measure: Restore populations to 18-22 historical lakes (Table 1; Fig. 1) 

approximately every 16 years after annual return rates to each Phase1 lake is at 

least 35 adult per acre for four successive years. 

6.2.1 Strategy: Use computer model (e.g., USFWS barrier model) to prioritize 

remaining lakes to be stocked by lake size, trophic status, number of downstream 

hydropower and nonhydropower dams, potential natural barriers, and distance to the 

ocean or to Milford Dam 9 . 

6.2.2 Strategy: Stock approximately six adult alewives per surface acre in remaining 

ponds using fish captured at Milford. 

8 Special techniques such as video monitoring may be needed at Howland. 

9 These are potential factors to be considered, and are not listed in order of priority. 

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Table 1. List of lakes above Veazie Dam believed to historically have had alewife 

runs (some Phase 3 lakes may be above natural barriers). Total hydro reflects the 

number of hydropower dams downstream of the waterbody after the removal of 

Veazie and Great Works and decommissioning of Howland. 

Surface 

Total Total 

River/ Stream Waterbody MIDAS Phase acres Stocking hydro nonhydro 

Blackman Chemo Pond 4278 1 1,146 6,876 0 2 

Pushaw Pushaw Lake 80 1 5,056 30,336 1 1 

Pushaw Little Pushaw Pond 2156 1 411 2,466 1 1 

Pushaw Mud Pond 2278 1 366 2,195 1 0 

Pushaw Boyd Lake 2158 1 1,005 6,030 1 1 

Passadumkeag Saponac Pond 4722 1 922 5,532 2 0 

Passadumkeag Madagascal Pond 2254 1 790 4,740 2 0 

Sebois Endless Lake 942 1 1,499 8,994 1 0 

Sebois Cedar Lake 2004 1 685 4,110 1 0 

Sebois East Branch Lake 2130 1 1,122 6,732 1 0 

Mattamiscontis Mattamiscontis Lake 2140 1 1,025 6,150 2 3 

Mattamiscontis Little Mattamiscontis Lake 2138 1 275 1,650 2 2 

Mattamiscontis South Branch Lake 2144 1 2,035 12,210 2 2 

Blackman Parks Pond 4272 2 124 744 0 3 

Blackman Davis Pond 4276 2 417 2,502 0 3 

Passadumkeag Eskutassis Pond 2250 2 876 5,256 2 2 

Passadumkeag Number Three Pond 9635 2 659 3,954 2 0 

Pleasant Ebeemee Lake 914 2 940 5,640 1 1 

Pleasant Upper Ebeemee Lake 966 2 196 1,176 1 1 

Pleasant Silver Lake 922 2 305 1,830 1 1 

Piscataquis Harlow Pond 2 595 3,570 3 3 

Penobscot Mattanawcook Pond 2226 2 832 4,992 2 2 

Penobscot Crooked Pond 2220 2 220 1,320 2 3 

Penobscot Folsom Pond 2222 2 282 1,692 2 3 

Cambolasse Snag Pond 2228 2 160 960 2 2 

Cambolasse Center Pond 2218 2 192 1,152 2 2 

Cambolasse Cambolasse Pond 2214 2 211 1,266 2 3 

Cambolasse Long Pond 2216 2 153 918 2 4 

Cambolasse Egg Pond 2216 2 128 768 2 4 

Cambolasse Caribou Pond 2216 2 544 3,264 2 4 

Mattakeunk Silver/Mattakeunk Lake 2242 2 570 3,417 2 3 

Molunkus Molunkus Lake 3038 2 1,050 6,300 2 0 

Molunkus Plunkett Pond 3056 2 435 2,610 2 0 

Molunkus Flinn Pond 3036 2 269 1,614 2 0 

Wytopitlock Wytopitlock Lake 1702 2 1,152 6,912 2 0 

WBr. Mattawankeag Matt'keag/ Up Matt'keag Lk 1686 2 3,330 19,980 2 0 

WBr. Mattawankeag Rockabema Lake 3636 2 339 2,034 2 2 

EBr. Mattawamkeag Skitacook Lake 2 435 2,610 2 0 

Baskahegan Upper Hot Brook Lake 1076 2 912 5,472 2 0 

Baskahegan Lower Hot Brook Lake 1072 2 713 4,278 2 0 

Baskahegan Crooked Brook Flowage 1082 2 1,645 9,870 2 1 

Baskahegan Baskhegan Lake 1078 2 6,944 41,664 2 1 

Mattaseunk Mattaseunk Lake 3040 2 576 3,456 2 0 

Salmon Salmon Stream Lake 3046 2 659 3,954 3 0 

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Table 1 (continued). List of lakes above Veazie Dam believed to historically have 

had alewife runs (some Phase 3 lakes may be above natural barriers). Total hydro 

reflects the number of hydropower dams downstream of the waterbody after the 

removal of Veazie and Great Works and decommissioning of Howland. 

Surface 

Total Total 

River/ Stream Waterbody MIDAS Phase acres Stocking hydro nonhydro 

Passadumkeag Cold Stream Pond 2146 3 3,628 21,768 1 1 

Passadumkeag Up Cold Stream Pond 2232 3 186 1,116 1 2 

Passadumkeag Nicatous Lake 4766 3 5,165 30,990 2 1 

Passadumkeag West Lake 503 3 1,344 8,064 2 1 

Passadumkeag Duck Lake 4746 3 256 1,536 2 1 

Passadumkeag Gassabias Lake 4782 3 896 5,376 2 1 

Sebois Seboeis Lake 954 3 4,201 25,206 1 1 

Schoodic Schoodic Lake 956 3 7,168 43,008 1 1 

Sebec Sebec Lake 848 3 6,803 40,818 2 1 

Kingsbury Piper Pond 298 3 420 2,520 4 0 

Penobscot Upper Pond 2230 3 506 3,036 2 4 

EBr. Mattawamkeag Pleasant Lake 1728 3 1,832 10,992 2 0 

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Figure 1. Alewife Phase 1 habitat (green) and other historical habitat (orange). Red 

circles are hydropower dams. Blue circles are presumed nonhydropower dams that 

require site visits for confirmation. 

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7.0 Objective: Rebuild the American shad population to self-sustaining levels 

in historical habitat within 50 years. 

7.1 Measure: Beginning in 2010 or 2011, restore approximately 633,300 American 

shad (Table 2) in 41-50 years by stocking 12 million hatchery-reared fry annually for 

41-45 years above Milford Dam, Howland Dam, and/or West Enfield Dam. 

7.1.1 Strategy: Identify potential sources of broodstock that could provide the 1000- 

1200 adults needed to produce 12 million fry. 

7.1.3 Strategy: Double capacity of Waldoboro shad hatchery. 

7.1.2 Strategy: Use in-basin shad as hatchery broodstock as soon as possible. 

7.1.4 Strategy: Develop an assessment plan per ASMFC protocols for evaluating the 

effectiveness of the hatchery stocking program and compared to . 

7.1.5 Strategy: Monitor adult shad returns by annual counts at Milford, West Enfield, 

and Howland 10 bypass and weekly biological sampling at Milford. 


barriers (see Passage and Connectivity objectives 16.1, 17.0, 18.0 and Non-native 

species objective 23.0 for timetables). 

7.1.7 Strategy: Conduct bi-weekly beach seine survey to assess juvenile fishes. 

7.1.8 Strategy: Conduct annual boat electrofishing survey to assess changes in 


7.1.9 Strategy: Cease fry stocking when at least 633,300 adult shad are passed at 

Milford for five years. 

7.2 Measure: Restore remaining reaches by allowing returning adults to pass 

upstream and reproduce naturally (if passage is effective) or truck fish returning 

adults upstream and allow to reproduce naturally. 

10 Special techniques such as video monitoring may be needed at Howland. 

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Table 2. River habitat that historically had shad, grouped by the number of post 

PRRT downstream hydropower dams. A plus (e.g. 2+) in the hydro dams column 

indicates that shad must utilize the Howland bypass in addition to passing the 

indicated number of hydropower dams. 

River reach 

Group 

production 

Production of 

adult shad % 

Post PRRT 

hydro dams 

Group 0 

Bangor Dam to Veazie Dam 22,344 1.4 0 

Veazie Dam to Great Works Dam 69,737 4.5 0 

Great Works Dam to Milford Dam 14,339 0.9 0 

106,420 

Group 1 

Milford Dam to West Enfield Dam 400,560 25.7 1 

Passadunkeag mouth to Lowell Dam 26,285 1.7 1 

Howland Dam to Dover-Foxcroft Lower Dam 153,461 9.8 1+ 

Pleasant mainstem and East Branch 37,769 2.4 1+ 

Pleasant West Branch 15,257 1.0 1+ 

633,331 

Group 2 

West Enfield Dam to Mattaceunk Dam 333,196 21.4 2 

Mattawamkeag mouth to Mattawamkeag Lake 205,744 13.2 2 

Lowell Dam to Saponic Pond 12,746 0.8 2 

D-F Lower to D-F Upper Dam 1,053 0.1 2+ 

552,739 

Group 3 

Mattaseunk Dam to Wassataquoik Stream 204,336 13.1 3 

Dover-Foxcroft Upper Dam to Guilford Dam 22,591 1.4 3+ 

226,927 

Group 4 

Mattaseunk Dam to Shad Pond 25,773 1.7 4 

Guilford Dam to Monson Junction 14,922 1.0 4+ 

40,695 

Total 1,560,111 1,560,111 

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8.0 Objective: Rebuild the blueback herring population to self-sustaining 


8.1.Measure: Every four generations (16 years) after Yr0 the blueback herring 

population above Milford will increase by 25% by natural reproduction of wild fish. 

8.1.1 Strategy: Monitor adult alewife returns by annual counts at Milford, West 

Enfield, and Pumpkin Hill fishways and Howland bypass, and weekly biological 

sampling at Milford. 


barriers (see Passage and Connectivity objectives 16.1, 17.0, 18.0 and Non-native 


8.1.3 Strategy: Conduct bi-weekly beach seine survey to assess juvenile fishes. 

8.1.4 Strategy: Conduct annual boat electrofishing survey to assess changes in 


8.1.5 Strategy: Truck a portion of blueback herring from Milford and release above 

Howland and West Enfield. 

9. 0 Objective: Rebuild the catadromous American eel population in historical 

habitat within 40 years. 

9.1. Measure: Five years after Yr0 the number of American eel recruits to the Milford 

headpond will increase by a factor of 10, and the relative abundance of American eel 

between Veazie and Milford will increase by a factor or 10. 

9.1.1 Strategy: Obtain daily counts of eel passage at Milford and weekly biological 

information (length and weight). 

9.1.2. Strategy: Assess and improve if needed upstream and downstream passage 

at barriers. 

9.1.3 Strategy: Use annual boat electrofishing survey to determine relative 

abundance and biomass of American eel in the river. 

10.0 Objective: Rebuild the sea lamprey population to self-sustaining levels in 

historical habitat within 40. 

10.1 Measure: Five years after Yr0 the number of sea lamprey migrating above the 

Milford headpond will increase by a factor of 10. 

10.1.1 Strategy: Obtain daily counts of sea lamprey at Milford and weekly biological 


10.1.2 Strategy: Assess and improve if needed upstream and downstream passage 

at barriers (see Passage and Connectivity objectives 16.1, 17.0, 18.0 and Nonnative 


11.0 Objective: Provide access for striped bass to historical habitat in the 

Penobscot River within 40 years. 

11.1 Measure: Create a recreational striped bass fishery above Milford in Yr1. 

11.1.1 Strategy: Obtain daily counts of striped bass at Milford and weekly biological 


PRFP Page 14

Work Plan Table 

The budget includes funding for one full-time Scientist and four 26-week 

Conservation Aides to restore 11 species of diadromous fish to the Penobscot. The 

Scientist will schedule, supervise, and participate in all work related to the 

restoration for these species. Tasks include counts of upstream diadromous 

migrants at Milford from May 1 – July 15, alewife stocking between May 1 and June 

15, obtaining shad broodstock and stocking fry from June 1 – July 31, and weekly 

beach seine survey from July 15 – September 30. Budget is estimated for 2010- 

2014. 

No. Action Timeline Responsibility Budget 

0.0 One full-time scientist, one full-time Specialist, 

four 26-week Conservation Aides 

2010-2014 DMR $882,362 

1.1.1 - 1.1.3; Estimate size of shortnose and Atlantic sturgeon 2007-2009 UM (ongoing) 

2.1.1 - 2.1.3 populations and identify critical habitat 

1.1.6; 2.1.6 Reassess sturgeon habitat 1-2 years after 2010-2012 PRRT/UM 

removal of Great Works and Howland 

(ongoing) 

3.1.1 Determine current rainbow smelt age structure 2011 DMR $15,600 

3.1.4, 4.1.3, 

6.1.6, 7.1.7, 

8.1.3 

Conduct beach seine survey for juvenile fish 2010-2014 DMR (staff in 0.0; 

equipment this 

line) 

6.1.1 Assess sources of alewife broodstock 2009-2010 DMR $0 

6.1.2 Stock alewives in phase 1 lakes 2010-2014 DMR (staff in 0.0; 

3 trucks/tank this 

line) 

$244,800 

6.1.7; 7.1.8; Conduct annual boat electrofishing survey 2010-2014 PRRT/UM 

8.1.4; 9.1.3 

(ongoing) 

7.1.2 Hatchery expansion 2010 DMR $590,000 

7.1 Produce 12M fry 2010-2014 DMR $1,061,827.16 

7.1 Stock 12 M fry 2010-2014 DMR (staff in 0.0; 

equipment in 

6.1.2) 

8.1.3 Develop hatchery assessment plan 2009 DMR $0 

6.1.4; 7.1.3; 

8.1.4; 9.1.1; 

10.1.1; 11.1.1; 

12.1.1 

Monitor returns of all species at Milford 2010-2014 DMR (staff in 0.0) 

$2,795,089 

PRFP Page 15 

$500

Work Plan Narratives 

1.1.1-1.1.3 and 2.1.1-2.1.2 Estimate the size of the shortnose sturgeon and 

Atlantic sturgeon populations, identify their essential habitat, and complete a 

genetic analysis. 

This work was initiated by the University of Maine in 2007, and is expected to be 

completed in 2010. The ongoing study uses acoustic telemetry, mark-recapture 

techniques, DIDSON sonar, and microsatellite DNA analysis to accomplish its 

objectives. The study is funded by a 4-year NOAA Section 6 grant to DMR. 

1.1.5 and 2.1.5 Estimate the size of the shortnose sturgeon and Atlantic 

sturgeon populations 20 and 40 years after Yr0. 

Population estimates should be made at least twice for both species after Veazie 

and Great Works dams are removed. Assuming that both species will be studied at 

the same time, the longer generation time of Atlantic sturgeon should drive the 

timing of the work. The shortnose sturgeon population, which overwinters in the 

Penobscot, could be assessed on a shorter cycle (14, 28, 42 years) if current studies 

using sonar (DIDSON) prove to be effective. 

1.1.6 and 2.1.6 Reassess essential habitat 1-2 year, 20 and 40 years after Yr0. 

Conduct a follow-up telemetry study 1-2 years after the removal of Veazie and Great 

Works dams are removed to determine whether sturgeon are utilizing the newly 

accessible habitat. Studies of habitat use should be made at least twice for both 

species after Veazie and Great Works dams are removed. Assuming that both 

species will be studied at the same time, the longer generation time of Atlantic 

sturgeon should drive the timing of the work. 

3.1.1 Document the age structure of the existing rainbow smelt population by 

2012 (or prior to Yr0). 

The current age structure should be documented. Declines in rainbow smelt 

populations in Massachusetts appear to co-occur with decreases in age at first 

spawning. 

3.1.2 Estimate the size of the rainbow smelt population in 2012(or prior to Yr0) 

if feasible. 

The most recent population estimate was developed from a mark-recapture study 

conducted nearly 40 years ago in conjunction with the commercial fishery. That 

fishery no longer exists, so a similar study would require a large amount of fishing 

effort. The existing or proposed assessment studies (rotary screw traps, beach 

seine survey, boat electrofishing) may not be useful for rainbow smelt. Newer 

techniques (e.g. hydroacoustics) or a combination of techniques might be more 

efficient, but the methodology would have to be developed. 

PRFP Page 16

3.1.3, 3.2.1, and 3.3.1 Estimate the size of the rainbow smelt population and 

assess its use of habitat between Veazie and Milford by Yr15; estimate the size 

of the population in Yr30 and Yr45. 

The size of the rainbow smelt population and its use of the habitat above Veazie 

should be determined approximately 15 years after the two lowermost dams are 

removed. Additional populations estimates should be made at 15 year intervals. 

New technology may be available in the future to make this assessment easier to 

accomplish. 

3.1.4, 4.1.3, 6.1.6, 7.1.6, and 8.1.3 Conduct biweekly juvenile fish survey. 

This would complement the surveys that have been occurring in the lower Kennebec 

and Androscoggin rivers since 1979 and the upper Kennebec since the removal of 

Edwards Dam. The biweekly beach seine survey provides information on multiple 

species, and is an ASMFC requirement for assessing juvenile alosines and striped 

bass on rivers undergoing restoration. 

4.1.1 Develop and institute a survey to assess trends in the Atlantic tomcod 

population and habitat use. 

The current distribution and abundance of the tomcod population is not known, and 

the existing or proposed assessment studies (rotary screw traps, beach seine 

survey, boat electrofishing) may not capture this species. Newer techniques (e.g. 

hydroacoustics) or a combination of techniques might be more efficient, but the 

methodology would have to be developed. 

4.1.2 Test tomcod periodically for mercury. 

Atlantic tomcod were used to determine the biological impact of mercury released 

from the HoltraChem site in Orrington. Mercury levels in tomcod tissue decreased 

downstream from site. Additional testing should occur after remediation is 

completed. 

4.1.3 Biweekly beach seine survey-see 3.1.4 

5.1.1 Identify sea-run brook trout populations in the Penobscot basin. 

At a minimum, populations of brook trout that have a sea-run component should be 

identified. 

PRFP Page 17

6.1 Restore alewife populations to Phase 1 historical lakes in 16 years or less 

beginning in 2010 or 2011. 

Alewife runs in lakes located above the Veazie Dam are considered extirpated, 

because of the presence of lake outlet dams 11 without fish passage, and ineffective 

passage for this species at Veazie and Great Works dams. DMR proposes to 

restore these runs by stocking six adults per surface acre, which has proven to be 

successful at many other locations in the state. Thirteen Phase 1 lakes have been 

selected initially for stocking because they 1) are close to sources of broodstock so 

travel is minimized, 2) have the smallest number of downstream hydropower dams 

so adult and juvenile mortality is reduced, 3) are blocked by the smallest number of 

nonhydropower dams so cost of improving upstream passage is minimized, 4) will 

allow testing of upstream and downstream passage efficiency at Milford, West 

Enfield, Howland, and Lowell Tannery within five years, and 5) will generate large 

runs that can be captured at Milford and serve as broodstock for restoring the 

remaining lakes. Chemo Pond, which is below Milford, is also on the list for stocking 

because fish passage will be completed in 2009, prior to dam removals. 

6.1.1 Assess availability and sufficiency of in-basin or nearest out-of-basin 

sources of broodstock. 

Approximately 97,500 adult alewife will need to be stocked annually in Phase 1 

lakes until returns are considered to be self-sustaining. The source of fish that will 

be used to stock these lakes has not yet been determined (Table 3) . DMR, NOAA, 

and USFWS will assess potential sources of broodstock based on the following 

criteria: 1) geographical proximity to historic habitat; 2) ability to provide 97,500 

adult alewife annually for up to 16 years without harm to the donor population; 3) 

facility for capturing, holding, and sorting broodstock; 4) availability of staff and 

equipment to transport and stock fish; and 5) costs and/or conflicts associated with 

existing resource users. With regard to geographical proximity, priority will be 

placed on using in-basin broodstock; other sources will be considered following the 

“next-nearest-neighbor” concept. A single, large donor stock capable of providing 

97,500 fish without impacting its long-term viability is preferred for logistical reasons. 

A facility where broodstock can be safely captured, sorted, and held for short periods 

of time will be necessary, and it will need to be operational no later than May 1, 

2011. DMR currently does not have available staff and equipment that can be 

dedicated to alewife stocking in the Penobscot drainage. However, biologists 

dedicated to the Kennebec and Androscoggin restoration projects regularly stock 

alewife from these watersheds into out-of-basin habitat; with a modest amount of 

additional funding, alewife from the Kennebec and/or Androscoggin rivers could be 

used to stock Phase 1 lakes in the Penobscot. If the agency assessment of sources 

of broodstock results in selection of a run that is commercially harvested, the 

municipality with rights to the run should be reimbursed for lost revenue. 

Continued analysis of the availability and feasibility of sources of broodstock will be 

conducted by DMR (Wippelhauser, Gray, Zink), NOAA (Saunders, Bernier), and 

11 Nonhydropower dams. 

PRFP Page 18

USFWS (Seavey). Analysis may include information on fish abundance and cost of 

obtaining additional abundance information; existence of current trapping facilities; 

and estimates of cost, timetable, and environmental impacts of alternative trapping 

facilities. The analysis will be completed by August 31, 2009. 

Table 3. Potential in-basin and out-of-basin sources of alewife broodstock. 

Location Run size Collection facilities/issues 

Veazie trap 2335 fish in 2009 Existing salmon trap; limited 

access during high flows; no 

existing shoreside facilities 

for handling 97,500 fish 

Souadabscook Unknown, sustainable 

harvest less than 97,500 

Orland Unknown, harvest less than 

97,500 in 7 of last 10 years 

Union 515,600 in 2008; harvest 

less than 97,500 in 3 of last 

10 years 

Kennebec 

(Lockwood) 

Androscoggin 

(Brunswick) 

Conflict with salmon 

broodstock collection 

No existing trap or shoreside 

collection facility. 

Existing tidal trap for 

commercial harvest. 

Competition with lobstermen 

for bait. 

Existing trap and shoreside 

facilities for commercial 

harvest and headpond 

stocking. 

Competition with lobstermen 

for bait 

131,201 fish in 2008 Existing trap and shoreside 

facilities for handling 97,500 

fish. 

92,359 fish in 2008 Existing trap and shoreside 

facilities for handling 97,500 

fish. 

6.1.2 Meet with lake associations prior to stocking new habitat. 

DMR must obtain a permit from DIFW to stock inland waters with alewife. DMR will 

meet with lake associations and Town officials at least one year prior to address 

concerns. 

6.1.3 Stock approximately six adult alewives per acre in Phase 1 lakes 

annually from 2010(2011) to 2026(2027) or until annual return rates are 

equivalent to at least 35 adult per surface acre for four successive years. 

PRFP Page 19

DMR has restored alewife runs throughout the State by stocking six adults per 

surface acre for at least one generation (four years). DMR considers runs to be selfsustaining 

when 35 adults per surface acre return to the spawning area annually, 

and estimates that stocking may have to continue for as many as four generations 

(16 years) to achieve that level of returns. Approximately 65 tankloads (1100 gallon 

tank) of fish will be needed to stock Phase 1 lakes (Table 4). 

Table 4. Number of fish to be stocked in Phase 1 lakes. 

Phase 1 lakes for 

restoration 

Number of 

tankloads 

Actual 

stocking 

Estimated 

production 

Chemo Pond 5 7,500 269,310 

Pushaw Lake 20 30,000 1,188,160 

Boyd Lake 4 6,000 236,175 

Little Pushaw Pond 2 3,000 96,585 

Mud Pond 1 1,500 85,972 

Endless Lake 6 9,000 352,265 

Cedar Lake 3 4,500 160,975 

East Branch Lake 4 6,000 263,677 

Saponac Pond 4 6,000 216,670 

Madagascal Pond 3 4,500 185,650 

South Branch Lake 8 12,000 478,225 

Mattamiscontis Lake 4 6,000 240,875 

Little Mattamiscontis Lake 1 1,500 64,625 

Total 65 97,500 3,839,164 

6.1.4 Monitor adult alewife returns by annual counts at Milford, West Enfield, 

Pumpkin Hill, and Howland and biological samples at Milford. 

Counts at each of the 12 Phase 1 lakes above Milford to determine whether the run 

is self-sustaining is not feasible. Monitoring annual adult returns at Milford and each 

of the four subdrainages being stocked (Pushaw, Passadumkeag, Piscataquis, 

mainstem above West Enfield) should be sufficient. Runs in Phase 1 lakes would be 

considered self-sustaining when annual adult returns are approximately 532,000 at 

Milford; 116,700 at West Enfield; 60,000 at Pumpkin Hill; and 115,700 at Howland or 

239,300 into Pushaw Stream. In addition, the presence of juveniles or juvenile 

emigration should be confirmed at each lake. 

Enumerating adult returns at these fishways will allow DMR to assess the status of 

the restoration, the timing of migrations, and passage effectiveness. 


6.1.7. and 7.1.7 and 8.1.4 and 9.1.2 Conduct annual boat electrofishing survey 

to assess changes in community structure. 

PRFP Page 20

A boat electrofishing survey (Yoder 2004) showed that Kennebec River between 

Augusta and Waterville/Winslow, which was restored to free-running state by the 

removal of Edwards Dam, was significantly more productive than the upstream 

impoundments. Because no sampling was conducted when Edwards Dam was in 

place, it is not possible to attribute the increased productivity to dam removal and 

river restoration. The longer timetable of the Penobscot Project has allowed similar 

electrofishing surveys to be conducted prior to the removal of Veazie and Great 

Works dams (Yoder 2005; NOAA 2008). These surveys will form the baseline for an 

annual survey to assess changes in the relative abundance and composition of the 

fish community. 

6.1.8 Use computer model to prioritize remaining lakes to be stocked. 

DMR has prioritized the lakes into three phases. Within these phases, lakes will be 

prioritized by lake size, trophic status, distance from the ocean, number of 

downstream hydropower dams, number of downstream nonhydropower dams, and 

feasibility 12 . The USFWS barrier model may be appropriate for this analysis. The 

barrier model has the advantage of incorporating the most recent barrier surveys as 

they are completed. 

6.2.1 Restore populations to 18-22 historical lakes 3 approximately every 16 

years by stocking six adult alewives per acre in remaining ponds using fish 

captured at Milford. 

When returns to Phase 1 lakes are greater than 35 adults per acre, the excess fish 

can be used as broodstock to restore runs to remaining historical habitat. Adult 

alewives will be captured at Milford fishlift and trucked to upstream habitat. 

7.1 Restore approximately 633,300 American shad in 41-50 years by stocking 

12 million fry annually for 41-45 years above Milford Dam, Howland Dam, 

and/or West Enfield Dam. 

American shad are extirpated above Veazie, because passage on the mainstem 

dams was not available for 130 years and the current fishway, installed in 1970, is 

ineffective at passing them. The size of the remnant shad population that inhabits 

the waters below Veazie Dam is unknown, although DMR has estimated it to be 

about 1000 adults, similar to the size of remnant populations on the Saco River 

(ME), Susquehanna River (PA, MD, NY), James River (VA), and St. John River 

(Canada). To date, no state or federal agencies or academic institutions have 

conducted or proposed to conduct a mark-recapture study that would be needed to 

obtain a population estimate. 

12 These are potential factors to be considered, and are not listed in order of priority. 

PRFP Page 21

During the development of the Operational Plan, DMR considered the likely success 

of passive (natural recolonization) versus active (stocking) shad restoration. In 

practice there are no examples of American shad populations in large rivers that 

have been restored or are being restored solely by natural recolonization. 

Restoration programs in Maine, New Hampshire, Massachusetts, Rhode Island, 

Virginia, Maryland and Pennsylvania have relied on stocking adults, juveniles, or fry 

to increase the abundance of shad. However, there are two examples in Maine 

where natural recolonization has resulted in a static shad population. On the Saco 

River where adult shad have simply been passed upriver the average run size for 16 

years is 1435 fish. On the Narraguagus River, counts of adult shad passing the 

single nonhydropower dam in each of three years (1987, 1989, 2007) have never 

exceeded 200 fish. 

DMR developed two models to explore scenarios that were likely to achieve shad 

restoration to estimated historical abundance in the 40-50 year time frame of this 

Operational Plan (8-10 shad generations). These models are simple, because there 

is a paucity of demographic data for shad populations in Maine as well as for shad 

populations along the Atlantic coast. 

The first model explored the possibility of achieving the restoration objective by 

natural recolonization; it uses a range of starting population sizes and intrinsic rates 

of increase from one generation to the next (Table 5). The model indicates that 

achieving Measure 7.1 (633,300 adult shad returns in 41-50 years) by natural 

recolonization would require either a very high rate of increase for a prolonged 

period or a very large starting population. For example, this target could be reached 

with a starting population of 2500-5000 fish that on average doubled in abundance 

every five years. This level of reproduction might be expected in bacteria, but not in 

shad. If the rate of reproduction is reduced to 1.5 or 1.25, the size of the starting 

population would have to be 40,000 to 135,000 fish. DMR is not aware of shad 

populations in Maine or elsewhere that consistently achieve these levels of 

reproduction nor of remnant populations on the east coast that have been greater 

than about 1000 fish. DMR has concluded that reliance on natural recolonization is 

not a valid management strategy. 

PRFP Page 22

Table 5. Results of natural recolonization model. 

Generational expansion rate = 2 Generational expansion rate = 1.5 

Year Population 1 Population 2 Population 4 Year Population 1 Population 2 Population 3 Population 4 

1 1,000 2,500 5,000 1 1,000 2,500 5,000 40,000 

6 2,000 5,000 10,000 6 1,500 3,750 7,500 60,000 

11 4,000 10,000 20,000 11 2,250 5,625 11,250 90,000 

16 8,000 20,000 40,000 16 3,375 8,438 16,875 135,000 

21 16,000 40,000 80,000 21 5,063 12,656 25,313 202,500 

26 32,000 80,000 160,000 26 7,594 18,984 37,969 303,750 

31 64,000 160,000 320,000 31 11,391 28,477 56,953 455,625 

36 128,000 320,000 640,000 36 17,086 42,715 85,430 683,438 

41 256,000 640,000 1,280,000 41 25,629 64,072 128,145 1,025,156 

46 512,000 1,280,000 2,560,000 46 38,443 96,108 192,217 1,537,734 

51 1,024,000 2,560,000 51 57,665 144,163 288,325 2,306,602 

56 2,048,000 56 86,498 216,244 432,488 3,459,902 

Generational expansion rate = 1.25 Generational expansion rate = 1.16 


1 1,000 2,500 135,000 1 1,000 2,500 135,000 225,000 

6 1,250 3,125 168,750 6 1,163 2,907 156,977 261,628 

11 1,563 3,906 210,938 11 1,352 3,380 182,531 304,218 

16 1,953 4,883 263,672 16 1,572 3,930 212,245 353,742 

21 2,441 6,104 329,590 21 1,828 4,570 246,797 411,328 

26 3,052 7,629 411,987 26 2,126 5,314 286,973 478,289 

31 3,815 9,537 514,984 31 2,472 6,179 333,690 556,150 

36 4,768 11,921 643,730 36 2,874 7,185 388,012 646,686 

41 5,960 14,901 804,663 41 3,342 8,355 451,176 751,960 

46 7,451 18,626 1,005,828 46 3,886 9,715 524,623 874,372 

51 9,313 23,283 1,257,285 51 4,519 11,297 610,027 1,016,712 

56 11,642 29,104 1,571,607 56 5,254 13,136 709,334 1,182,223 

Measure 7.1: 633,300 adult shad returns in 35-40 years 

DMR next modeled restoration at two fry stocking levels (Table 6). The model 

assumes one adult return for each 318 hatchery fry released and 100 adult returns 

for each 86 spawning adults (intrinsic rate of increase from one generation to the 

next = 1.16) based on data presented in Restoration of American Shad to the 

Susquehanna River: Annual Progress Report 2000. The model indicates that 12 

million fry would need to be stocked annually for 41-45 years to achieve a population 

of 633,300 adults in 41-50 years. 

PRFP Page 23

Table 6. Results of model showing adult returns from A) stocking 6 million fry 

annually and B) stocking 12 million fry annually. 

A. 

Fry stocking years 

Return Total annual Y1-5 Y6-10 Y11-15 Y16-20 Y21-25 Y26-30 Y31-35 Y36-40 Y41-45 Y46-51 

years adult returns 6,000,000 6,000,000 6,000,000 6,000,000 6,000,000 6,000,000 6,000,000 6,000,000 6,000,000 6,000,000 

Y6-10 18,868 18,868 

Y11-15 40,807 21,939 18,868 

Y16-20 66,318 25,511 21,939 18,868 

Y21-25 95,982 29,664 25,511 21,939 18,868 

Y26-30 130,475 34,493 29,664 25,511 21,939 18,868 

Y31-35 170,583 40,108 34,493 29,664 25,511 21,939 18,868 

Y36-40 217,221 46,637 40,108 34,493 29,664 25,511 21,939 18,868 

Y41-45 271,450 54,229 46,637 40,108 34,493 29,664 25,511 21,939 18,868 

Y46-50 334,508 63,057 54,229 46,637 40,108 34,493 29,664 25,511 21,939 18,868 

Y51-55 407,830 73,323 63,057 54,229 46,637 40,108 34,493 29,664 25,511 21,939 18,868 

Y56-60 474,221 85,259 73,323 63,057 54,229 46,637 40,108 34,493 29,664 25,511 21,939 

Y61-65 551,420 99,138 85,259 73,323 63,057 54,229 46,637 40,108 34,493 29,664 25,511 

Y66 641,186 115,277 99,138 85,259 73,323 63,057 54,229 46,637 40,108 34,493 29,664 

B. 


Return Total annual Y1-5 Y6-10 Y11-15 Y16-20 Y21-25 Y26-30 Y31-35 Y36-40 Y41-45 Y46-51 

years adult returns 12,000,000 12,000,000 12,000,000 12,000,000 12,000,000 12,000,000 12,000,000 12,000,000 12,000,000 

Y6-10 37,736 37,736 

Y11-15 81,615 43,879 37,736 

Y16-20 132,637 51,022 43,879 37,736 

Y21-25 191,965 59,328 51,022 43,879 37,736 

Y26-30 260,950 68,986 59,328 51,022 43,879 37,736 

Y31-35 341,167 80,216 68,986 59,328 51,022 43,879 37,736 

Y36-40 434,441 93,275 80,216 68,986 59,328 51,022 43,879 37,736 

Y41-45 542,900 108,459 93,275 80,216 68,986 59,328 51,022 43,879 37,736 

Y46-50 669,015 126,115 108,459 93,275 80,216 68,986 59,328 51,022 43,879 37,736 

We are proposing to stock shad into habitat above Milford, West Enfield, and 

Howland as soon as possible to allow testing of upstream and downstream passage 

efficiency at Milford, West Enfield, and Howland, and Lowell Tannery within five 

years of stocking. American shad are proving to be one of the most difficult 

anadromous species to successful pass at technical fishways, and an early 

determination of passage efficiency at Milford and Howland is critical to shad 

restoration on this river. If adult shad use the state-of-the-art fishlift that will 

constructed at Milford, they can be serve as broodstock for the hatchery and/or can 

be passed upstream to spawn naturally. 

7.1.1 Identify potential sources of American shad broodstock (500-600 adults 

to produce 6M fry or 1000-1200 adults for 12M fry). 

The privately owned Waldoboro Shad Hatchery, which has provided fry for the 

Kennebec River Restoration Project, was modeled after the Pennsylvania Fish and 

Boat Commission Hatchery that has successfully supplied shad for the 

Susquehanna River restoration. The Waldoboro Hatchery currently requires 500- 

600 adult shad broodstock to produce up to 6 million fry. At the start of the season, 

DMR trucks several hundred adult broodstock to the hatchery. The fish are allowed 

to spawn naturally in large indoor circular tanks; no hormones are used in this 

process. DMR trucks additional fish to the hatchery, which are added to the 

spawning tanks to compensate for spawning mortality or to replace spent fish. 

Fertilized eggs are collected, allowed to hatch, and transferred to fry tanks. Fry are 

fed, marked with OTC, and released into the river when they are approximately 21days 

old. 

PRFP Page 24

Because adult shad mortality increases with increasing temperature and distance 

that fish must be trucked, only sources of broodstock within a 5-6 hour drive were 

considered. Potential sources of sufficient broodstock in the Gulf of Maine are 

limited (Table 7). A remnant population exists in the lower Penobscot, but DMR 

estimates this population to be 1000 fish at most. In addition, capturing these fish 

for broodstock before the removal of Veazie and Great Works dams would be nearly 

impossible. Runs in the other Maine rivers are either too small, are undergoing 

restoration, or cannot be easily captured. The nearest source 13 of 1000-1200 adults 

within the Gulf of Maine is the Merrimack River (Table 7). This quantity of 

broodstock is also available from the Connecticut River, located outside the Gulf of 

Maine. 

During the development of this operational plan, we reviewed the best available 

information regarding the genetic structuring of shad populations on the east coast in 

order to assess the potential impacts of using out-of-basin shad broodstock for the 

Penobscot River restoration. This analysis is presented in Appendix A. 

Table 7. Nearest potential sources of American shad broodstock. 

River system Distance Status of run 

Penobscot 0 mi Size unknown, not easily captured 

Kennebec/Androscoggin 58 mi Size unknown, ongoing restoration, not easily 

captured 

Narraguagus 72 mi 100 adults in 2008 

Saco 93 mi ~1200 adults, ongoing restoration, capture at 

fishlift 

Merrimack 125 mi ~29,000 in 2008, ongoing restoration, capture 

at fishlift 

St. John 179 mi Less than 1000 in 28 of 29 years from 1974- 

2002 

7.1.2. Double capacity of Waldoboro American shad hatchery. 

The Waldoboro Shad Hatchery currently can produce up to 6 million fry per year. It 

would have to be expanded to produce 12 million fry per year, which could be 

accomplished in less than one year if funding becomes available. 

7.1.3 Develop an assessment plan for evaluating the effectiveness of the 

American shad hatchery stocking program (per ASMFC protocols). 

Amendment 1 to the Interstate Fishery Management Plan for Shad and River 

Herring requires that states with a hatchery program must submit proposals for 

evaluation and provide information in the annual report of the hatchery contribution 

(percent wild versus hatchery fish for juveniles and adults). Most programs mark 

hatchery fry with OTC, which shows as a fluorescent ring on the otolith. Samples of 

emigrating juveniles and returning adults are sacrificed and their otoliths are 

13 Distance measured from river mouth to river mouth. 

PRFP Page 25

examined for the OTC mark. An assessment plan will be developed and submitted 

to the Atlantic States Marine Fisheries Commission prior to stocking. 

7.1.4 Monitor adult returns by annual counts-see 6.1.4 


7.1.7 Conduct annual boat electrofishing survey-see 6.1.7 

8.1. Every four generations (16 years) after Yr0 the blueback herring 

population above Milford will increase by 25% by natural reproduction of wild 

fish. 

Blueback herring above the Veazie Dam are considered extirpated, because of the 

ineffective passage for this species at Veazie and Great Works dams. DMR 

proposes to restore these runs by natural reproduction. Blueback herring spawn in 

rivers like American shad, but appear to have a high intrinsic rate of reproduction like 

alewife. Blueback herring were not actively managed on the Kennebec River, that is 

no stocking occurred, but wild fish have been documented spawning at numerous 

locations in the newly accessible reach above Augusta. Blueback herring that are 

captured at Milford will either be passed upstream or trucked to habitat above a 

mainstem dam and released so passage effectiveness can be tested. 




8.1.5 Truck a portion of blueback herring from Milford and release above 

Howland and West Enfield. 

Trucking a portion of adults upstream will allow assessment of passage efficiency at 

the mainstem dams for blueback herring. 

9.1.1 Monitor eel recruitment by daily counts at Milford and weekly biological 



Determine if apparent decline in abundance of young-of-year between Bangor Dam 

and Veazie Dam continues after dam removals. 


PRFP Page 26

11.0 Rebuild the striped bass population in historical habitat within 40 years. 

There is no evidence that striped bass historically spawned in the Penobscot River 

as they did in the Kennebec, nor is there evidence that they currently spawn in the 

Penobscot. It is likely that striped bass arriving in the Penobscot are fish from 

southern spawning populations on a summer feeding migration. 

References 

Fernandez, S.J. 2008. Population demography, distribution, and movement patterns 

of Atlantic and shortnose sturgeons in the Penobscot River estuary, Maine. M.S. 

Thesis. University of Maine, Orono, ME. 100 pp. 

NOAA Fisheries. 2008. Penobscot River fish assemblage survey interim report. 

Woods, Hole MA and Orono, ME. Prepared by Kleinschmidt Associates. 84 pp. 

Yoder, C.O., B.H. Kulik, and J.M. Audet. 2004. Maine rivers fish assemblage 

assessment: Interim Report. Kennebec River: 2002 and 2003, Androscoggin River: 

2003, Sebasticook River 2003. Midwest Biodiversity Institute Center for Applied 

Bioassessment & Biocriteria, Columbus, OH 43221; Kleinschmidt Associates, 

Pittsfield, ME 04967. 205 pp. 

Yoder, C.O., B.H. Kulik, and J.M. Audet. 2005. Maine rivers fish assemblage 

assessment: Interim Report II. Penobscot River and tributaries: 2004. Midwest 

Biodiversity Institute Center for Applied Bioassessment & Biocriteria, Columbus, OH 

43221; Kleinschmidt Associates, Pittsfield, ME 04967. 94pp. 

PRFP Page 27

Atlantic Salmon 

Authors: Oliver Cox, Norm Dubé, Greg Mackey, and Randy Spencer 

Introduction 

Recovery of self-sustaining populations of Atlantic salmon is central to the mission of 

MDMR, federal agencies, PIN, and other partners. Natural spawning is fundamental 

to recovery, genetic viability, and long-term persistence of self-sustaining 

populations. The emphasis for this operational plan is to increase natural spawning 

and wild recruitment. However, wild Atlantic salmon populations that are only 

supported by natural spawning (e.g. Ducktrap River, Cove Brook, Souadabscook 

Stream) continue to falter. Pending improvement in marine survival rates and 

freshwater production, hatchery supplementation will continue to play a vital role in 

an integrated management approach. Thus, this plan also emphasizes strategies to 

improve the quality and survival of hatchery products. In the Penobscot River, low 

numbers of returning adult Atlantic salmon combined with ineffective upstream 

dispersal contribute to chronic under utilization of available spawning habitat. Most 

Penobscot broodstock originated as hatchery origin stocked smolts, and most of 

those smolts (99.2% ± 0.4 SE, 2001-2007 mean) had at least one hatchery origin 

parent. Maintaining the fitness of hatchery broodstock is a high priority. Increasing 

returns of wild origin broodstock (through increased natural spawning and wild smolt 

escapement) will reduce the potential for multiple successive generations of 

hatchery influence and contribute to broodstock fitness. 

This operational plan will build on the suite of existing management actions and 

recent program reviews (e.g. NRC 2004, Fay et al. 2006, and SEI 2007) 

incorporated in the Strategic Management Plan (SMP). Management actions with 

potential for rapid and tangible population level responses are identified. Population 

effects may be quantitative or qualitative (e.g. genetic) but actions with the potential 

to produce both are given a higher priority. Populations are most sensitive to 

manipulation of advanced life stages (adults and smolts) and these actions are also 

given high priority. Effective adult escapement (the number that spawn successfully) 

is driven by the total number of returns, the proportion extracted for hatchery 

broodstock, and the performance of spawners in the river. Spawning performance is 

influenced by habitat quality, habitat accessibility, and spawner fitness. The number 

of adult returns is driven by smolt escapement and survival. Smolt escapement is a 

function of total production less migratory losses, which in turn is influenced by 

environmental conditions (e.g. dams, predator abundance) and by smolt quality. 

Proposed actions to increase freshwater production, survival, and reproductive 

success are presented for both wild and hatchery fish. 

Background 

There is little information on the historic population structure of Atlantic salmon in the 

Penobscot basin and currently the Penobscot basin is managed as a panmictic 

PRFP Page 28

meta-population. Based on watershed geography and estimates of habitat quantity, 

coupled with theories of Atlantic salmon homing and straying, it is reasonable to 

assume that sub-populations existed in the Penobscot basin. The Penobscot River 

basin consists of at least six sub-drainages upstream of, and four downstream of the 

Veazie Dam. The potential for environmentally driven adaptations conveying fitness 

unique to sub-drainage has not been assessed in the Penobscot. However, 

research elsewhere provides growing support for the concept of heritable withinbasin 

adaptation in smolt run timing and other fitness related characteristics. 

Assessing the potential for the existence or creation of locally adapted subpopulations 

and predicting their viability would assist in developing long term 

management strategies. 

Where production potentials are equal, reaches with the fewest dams impeding 

upstream and/or downstream migration will be more likely to produce self-sustaining 

Atlantic salmon populations. Optimizing reach specific smolt recruitment will require 

an appropriate balance between dam related losses and production potential 

(amount and quality of available habitat). Quantitative data (e.g. habitat productivity, 

downstream mortality) necessary to inform those decisions are limited, but still 

provide insight. Available data were used to model both productive potential and the 

potential effects of dam related mortality on population viability (Appendix B). 

Juvenile Atlantic salmon rearing habitat in the Penobscot basin was estimated using 

both field survey data and data from a GIS-based Atlantic salmon habitat model 

developed by USFWS and NOAA (Wright et al. 2008). Habitat data were 

aggregated at several spatial scales within the basin, including Dam Reach, 

Management Reach, and HUC 10. The data used are available as an ARCMap 

geo-database. The goals of the modeling were to 1) provide the best available 

information on Atlantic salmon rearing habitat in the Penobscot basin, 2) provide an 

estimate of the relative potential for large parr production in the basin, and 3) identify 

reaches with the highest parr production potential (Appendix B). The production 

model combined with the Atlantic salmon population viability by reach model 

(Appendix C) helps identify data gaps requiring focused research and facilitate 

management decisions. 

Adaptive management is a structured decision process that will be used to govern 

implementation and modification of the operational plan. Its utility is to ensure that 

management decisions and actions are modified, discontinued, or perpetuated 

based on cause and effect relationships. Adaptive management relies on 

establishing management plans based on a priori hypotheses (predicted results), 

assessment plans to collect data necessary to evaluate a management strategy, and 

a feedback mechanism to inform and improve management as results are obtained. 

The guidance document for Adaptive Management in the Basin is located in 

Appendix D. 

Atlantic salmon enhancement strategies that can be used in the Penobscot River to 

augment in-river production and adult returns include (Appendix E): 

1. Egg planting 

PRFP Page 29

2. Streamside incubation 

3. Fry stocking 

4. Parr stocking (graded pre-smolts, ambient fall parr) 

5. Smolt stocking 

6. Trap and truck sea-run adults to ensure access to quality habitat 

7. Captive-reared adult stocking 

8. Rejuvenated kelt stocking 

9. No stocking - natural reproduction only 

Fry, parr, and smolt stocking are the standard enhancement practices in the 

Penobscot watershed. The contribution of hatchery smolt stocking to adult returns is 

well documented but the relative effectiveness of other enhancement methods is 

poorly characterized. Research to address these data gaps is prioritized and will 

focus on fry, parr, (and smolt) stocking treatments and assessments. Trap and truck 

(adult translocations) will also be investigated as a means of increasing the effective 

spawning escapement of returning adults. Evaluations of streamside incubation, 

egg planting and captive-reared adult releases are currently in progress in other 

Maine rivers. Some or all of these enhancement techniques may have future 

application in the Penobscot program. 

Strategies to Increase Adult Escapement to the Penobscot Basin 

Increasing spawning escapement to upstream reaches is a prerequisite for recovery 

of salmon populations in the Penobscot River. Currently adult Atlantic salmon 

escapement is limited by several critical factors: 

1. Low number of returning adults from all sources (natural spawning and 

stocked smolt, fry, and parr). 

2. Six hundred and fifty sea-run adults are removed annually to meet hatchery 

broodstock needs for the fry, parr, and smolt stocking programs. 

3. Upstream fish passage facilities are not 100% effective and impede adult 

escapement upstream. Level of impact is dependent on the number of dams 

ascended, fish passage facility effectiveness, and environmental conditions. 

Operational Objectives 

The objectives presented here provide a link between the objectives in the SMP and 

the tasks within the operational plan. Most of the tasks within the operational plan 

relate to strategic objectives 4 (achieve self-sustaining smolt to adult return rates) 

and 5 (achieve interim juvenile life stage-specific measures) (Appendix F). Both of 

those objectives are derived from strategic objective 2 (Increase natural spawning). 

Each task within the operational plan has been associated with one operational 

objective, but may be related to others. Inherent with each objective is the need to 

assess our management actions and report our findings. Appropriate operational 

measures will be associated with each strategy to evaluate the action and inform the 

adaptive management process. 

PRFP Page 30

Objective 12: Increase wild/natural spawning 

• 12.1 Strategy- Define the best use (disposition) of Atlantic salmon adult 

returns based on origin, age, run timing, and stocking needs. 

• 12.2 Strategy- Reduce Broodstock requirement by collection 

alternative life stages (parr or smolts) and rear to adults to supplement 

sea-run broodstock requirements and or adult escapement 

• 12.3 Strategy- Reduce Broodstock requirement by spawning additional 

life stages (precocious parr) 

• 12.4 Strategy- Rejuvenate kelts to augment hatchery broodstock and 

spawning escapement 

• 12.5 Strategy- Improve fish passage to effectively increase adult 

spawners upstream 

• 12.6 Strategy- Adult Atlantic salmon translocation to increase and 

aggregate spawning escapement into quality habitat 

Objective 13: Increase juvenile survival 

• 13.1 Strategy- Increase the quality of hatchery products (e.g., genetic, 

physical, physiological, behavioral) through improved rearing practices, 

conditioning, and broodstock fitness 

• 13.2 Strategy- Improve stocking methods (where, when and how) to 

increase survival of the hatchery product 

• 13.3 Strategy- Assess environmental conditions that maximize survival 

of hatchery products 

• 13.4 Strategy- Improve habitat quality and complexity (e.g., physical, 

chemical, ecological) to maximize salmon production (See Section 3 

and Appendix G) 

• 13.5 Strategy- Increase connectivity to quality habitat to maximize 

salmon production (See Section 2) 

Objective 14: Increase smolt to adult survival 

• 14.1 Strategy- Circumvent marine mortality by captive-rearing wild 

smolts to maturity (e.g. sea-cage rearing) and release pre-spawning in 

to superior habitat 

• 14.2 Strategy- Stock smolts in locations and at times that maximizes 

returns rate 

• 14.3 Strategy- Improve downstream passage efficiency for smolts 

Objective 15: Increase the number of hatchery Atlantic salmon stocked 

• 15.1 Strategy- Increase or reallocate hatchery production to increase 

the production of high returning products (i.e., more smolts) 

Operational Measures 

The operational measures listed below will be used to evaluate the success of 

individual tasks through life stage-specific measures. Interim life-stage measures 

PRFP Page 31

provide timely feedback and evaluation of management actions. Assessment of 

each measure should use appropriate data collected using standard methods. 

• Egg Deposition: On average, ≥ 240 egg deposition per 100 m 2 stream 

habitat 

• Fry Production: On average, ≥ 19 fry per 100 m 2 stream habitat (240 

eggs/unit*0.08) 

• Parr Production: On average, ≥ 6 parr per 100 m 2 stream habitat (240 

eggs/unit*0.025), ≥ estimates from cumulative drainage area 

regression model, or ≥ known production 

• Smolt Production: On average, ≥ 3 smolts per unit (240 

eggs/unit*0.0125), ≥ estimates from parr regression, or ≥ known smolt 

production 

• Freshwater Survival: Egg to smolt survival of ≥ 1.25% (fry to smolt 

survival of ≥ 15.8%) 

• Relative Survival or Production: 

o Compare hatchery verses wild survival, population densities 

and/or smolt production 

o Compare survival or production to previous MDMR data for 

relative measures of success 

PRFP Page 32


The budget includes funding for five full-time Biologists, two full time Biology 

Specialists, two seasonal Conservation Aides and six seasonal contract workers. 

Budget is estimated for 2010-2014. 


12.0.1 Write Semi-annual NOAA Reports May & Nov. MDMR $83,520 

12.0.2 

Hold annual Penobscot Atlantic salmon 

assessment workshop to integrate and 

analyze stocking, habitat, telemetry, 

passage, and population data January MDMR $60,840 

12.0.3 Write Annual Penobscot Report January MDMR 

MDMR, 

$40,560 

Develop Broodstock Management Plan 

USFWS, 

12.1.1 (BSMP) 

Evaluate the best use (disposition) of 

Feb-10 NOAA $16,544 

returning wild and hatchery origin Atlantic 

MDMR, 

salmon captured at the Veazie Dam fishway 

USFWS, 

12.1.2 trap Feb-10 NOAA $2,068 

12.1.3 

12.1.4 

Update and revise Penobscot adult Atlantic 

salmon collection protocol Feb-10 MDMR $1,908 

Operate the adult Atlantic salmon collection 

facility according to standard operation 

procedures (SOP) Annual MDMR $440,192 

12.1.5 

Develop and implement a standardized redd 

count sampling scheme Apr-10 MDMR $16,544 

12.1.6 Monitor reaches for natural re-colonization May-09 MDMR $18,100 

12.1.7 

12.1.8 

12.2.1 

12.3.1 

12.4.1 

12.5.1 

12.6.1 

Monitor 2008 redds to evaluate spawning 

success (YOY) 

Investigate recruitment from natural 

spawning relative to other enhancement 

Aug-09 MDMR $6,752 

strategies Jan-11 MDMR $45,792 

Supplement sea-run broodstock needs with 

alternative broodstock sources (parr, smolts) 

with the goal of increasing sea-run adult 

escapement (e.g. alternative broodstock 

sources, reviewing production needs, 

evaluation hatchery production potential) Feb-10 

Review methods and ideas for using 

precocious parr in addition to adults as 

broodstock Feb-10 

MDMR, 

USFWS, 

NOAA $2,068 

MDMR, 

USFWS, 

NOAA $2,068 

Review the potential to rejuvenate kelts, and 

identify possible uses (e.g. broodstock, 

spawning escapement) Jan-12 MDMR $1,908 

Collaborate with PPL, PRRT, and federal 

agencies to assess the Milford fish lift 2011-2014 MDMR et al. $5,724 

Proposal to investigate natural spawning 

performance of translocated adult salmon Apr-09 MDMR $15,264 

PRFP Page 33

13.1.1 

13.1.2 

13.2.1 

13.2.2 

13.2.4 

13.2.5 

13.2.6 

Literature review evaluating causes and 

remedies for poor performance of hatchery 

fry relative to wild fry Jan-10 MDMR $1,908 



smolts relative to wild smolts May-09 MDMR $3,816 

Develop an integrated stock enhancement 

program to optimize adult Atlantic salmon 

returns Feb-10 MDMR $16,544 

Develop and implement an integrated 

assessment plan Apr-10 MDMR $82,720 

Develop and implement a standardized 

juvenile assessment scheme Apr-10 MDMR $82,720 

Proposal to expand MDMR egg planting 

research into the Penobscot Jan-10 MDMR $3,816 

Develop a fry stocking adaptive management 

plan Feb-10 MDMR $7,632 

13.2.7 

Review and assess causes and remedies for 

poor natural recruitment Dec-10 MDMR $3,816 

13.2.8 Report: Juvenile production from fry stocking Dec-10 MDMR $3,816 

13.2.9 

13.2.10 

13.2.11 

13.2.12 

13.2.13 

13.2.14 

13.2.15 

Stock fry and assess according to existing 

management practices Apr-09 MDMR $168,800 

Stock fry according to fry stocking adaptive 

management plan 

Evaluate alternative fry stocking 

strategies/locations to increase smolt 

2010 -2014 MDMR $675,200 

production Jan-11 MDMR $45,792 

Develop a parr stocking adaptive 

management plan Feb-10 MDMR $7,632 



parr relative to wild parr Jan-10 MDMR $3,816 

Stock parr and assess according to existing 

management practices Sep-09 MDMR $84,400 

Stock parr according to parr stocking 

adaptive management plan 2010 -2014 MDMR $337,600 

13.2.16 

Report current stocking practices (fry, parr, 

smolts, adults), documenting decisions for 

annual allocations for each life stage Apr-09 MDMR $19,080 

13.2.17 Assess hatchery product marking scheme 

Review and develop habitat based 

productivity estimates, integrating fry and 

parr performance, habitat data, and water 

Jul-09 MDMR/NOAA $2,068 

13.3.1 quality Feb-10 MDMR $16,544 

14.1.1 

Evaluate smolt stocking strategies to 

minimize smolt mortality Apr-09 USFWS/MDMR $3,816 

PRFP Page 34

14.1.2 

14.1.3 

14.2.1 

14.2.2 

14.2.3 

14.3.1 

14.3.2 

15.1.1 

Proposal to evaluate environmental 

conditioning of smolts (e.g. freshwater smolt 

ponds and sea-cages) to improve survival 

during transition to the marine environment Dec-09 USFWS/MDMR $2,068 

Proposal to capture and captive rear in seacages 

wild and/or naturally-reared Penobscot 

smolts for release as sexually mature adults 

in selected river reaches Dec-09 MDMR $4,136 

Develop a smolt stocking adaptive 

management plan Feb-10 MDMR $7,632 

Stock smolts and assess according to 

existing management practices May-09 MDMR $84,400 

Stock smolts according to smolt stocking 

adaptive management plan 2010 -2014 MDMR $337,600 

Proposal to evaluate downstream smolt 

passage efficiency in the Piscataquis River Jan-10 MDMR $1,908 

Discuss with PRRT the possibility of testing 

downstream passage measures (e.g. 

manipulate operating regimes) at PRRT 

owned dams prior to dam removal Apr-10 

MDMR & 

PRRT $1,908 

Assess feasibility of increasing or reallocating 

hatchery smolt production to produce more 

adult returns Feb-10 MDMR $1,908 


12.0.1 Write Semi-annual NOAA Reports 

A variety of tasks included in this plan are funded by NOAA under elements of a 

cooperative agreement for Atlantic Salmon Freshwater Assessments and Research 

of Mutual Interest to Maine Department of Marine Resources Bureau of Sea Run 

Fisheries and Habitat. In June and November, a report on NOAA funded work 

completed in the previous six months must be submitted to the project officer. The 

primary tasks that are common to the cooperative agreement and this Plan are: 

collecting and analyzing data on the biological characteristics (e.g. age, size, origin, 

condition) of adult salmon captured and enumerating all species trapped at the 

Veazie Dam, collecting and transporting Atlantic salmon broodstock to Craig Brook 

National Fish Hatchery, assessing alternative stocking strategies for Atlantic salmon, 

estimating age, origin, and numbers of juveniles and smolt produced at sites within 

the drainage, surveying for spawning activity, and acquiring temperature, water 

quality, and physical habitat data. 

12.0.2 Hold annual Penobscot Atlantic salmon assessment workshop to 

integrate and analyze stocking, habitat, telemetry, passage, and population 

data 

Hold an annual assessment workshop for the Penobscot River. The focus will be on 

developing assessments and analyses that will provide useful feedback to the 

PRFP Page 35

adaptive management structure. Results will be assessed in terms of relevant shortterm 

measures, and more importantly, in terms of the overarching plan objectives 

and measurable demographic rates. Initially, these meetings will focus more heavily 

on developing assessments and analyses, while performing the analyses and 

deriving management recommendations will be the primary focus. The group will 

produce documents annually describing their work and meet with managers to 

inform the adaptive management process. The core team will consist of the BSRFH 

Biologist working on the Penobscot. Other participants that the team believes can 

assist in and improve their work will be invited. The idea is for the team to function 

efficiently as a streamlined workgroup. Broader participation should be achieved 

with informational meetings and documents. 

12.0.3 Write Annual Penobscot Report 

An annual report will be produced that summarizes MDMR activities in the 

Penobscot drainage. The report is part of our efforts to document our management 

and research activity, report results, and document management actions based on 

those results. 

12.1.1 Develop Broodstock Management Plan 

Develop criteria and for disposition of adult Atlantic salmon trapped at the Veazie 

Dam fishway trap and subsequently the Milford Fish lift once operational. The 

Broodstock management plan (BSMP) requires an expanded section on Penobscot 

broodstock management. This task will be carried out by the Genetic Diversity 

Action Team (GDAT). The plan should cover all aspects of the Penobscot 

broodstock, including but not limited to alternate sources (life stages) of broodstock, 

target numbers, proportion of hatchery and wild fish in the broodstock, best use and 

management of the F2 line, effective population size issues, and domestication 

issues. This task is currently in the list of tasks under the GDAT. 

12.1.2 Evaluate the best use (disposition) of returning wild and hatchery origin 

Atlantic salmon captured at the Veazie Dam fishway trap 

Naturally spawning wild Atlantic salmon are the most important step toward restoring 

Atlantic salmon to the Penobscot River. However, the low numbers of fish and low 

survivals, coupled with the desire to minimize divergence of conservation hatchery 

and wild fish complicate the use of wild adults. Any strategy developed under this 

task will need to be fully compatible with the Broodstock Management Plan and will 

need to be vetted through the GDAT. Assemble a small team to review information 

and develop ideas. 

12.1.3 Update and revise Penobscot adult Atlantic salmon collection protocol 

Adult Atlantic salmon collection protocols will need to be updated to reflect changes 

in the BSMP and the collection facility at Milford. The protocol will be adapted and 

updated from current protocols used at the Veazie Dam fishway trap and other lifts 

in the State. Safeguards that are in place to protect Atlantic salmon should not 

change. We anticipate that procedures related to the operation of the new lift and 

the logistics of the location will change. 

PRFP Page 36

12.1.4 Operate the adult Atlantic salmon collection facility according to 

standard operation procedures (SOP) 

MDMR is currently managing the Veazie Dam adult trap according to current adult 

salmon trap protocols. The trap is operated annually from May 1 st to October 31st. 

Operations will follow the most current SOP. The SOP is expected to change based 

on recommendations in the BSMP as well as a change in the collection location 

(Tasks 12.1.1). 

12.1.5 Develop and implement a standardized redd count sampling scheme 

Assessment of adult returns, movement, and reproductive success requires an 

unbiased and spatially representative sample (see Appendix H, Task 13.2.2). 

Sampling should consider for trend and status analysis. In addition, sampling should 

allow for greater effort depending on the assessment needs of biologists and 

managers. Finally, sampling must be flexible to allow un-sampled sites to be 

accounted for, and to add sites as needed. Collecting redd data under an integrated 

probabilistic sampling plan with standardized protocols should increase statistical 

power, focus sampling efforts, and allow analysis at various spatial and temporal 

scales. The redd sampling plan for the Penobscot will be the core for a larger statewide 

sampling plan. The sample plan will also include procedures for repeated 

counts and timing of counts. The sample will be spatially balanced and will 

accommodate varying sampling effort and needs across space. When appropriate, 

field methods for research projects should conform to this standardized sampling 

scheme. 

12.1.6 Monitor reaches for natural re-colonization 

Monitor reaches for natural re-colonization (areas with no active stock enhancement) 

by juvenile assessment and redd surveys on an annual basis. Ideally, vacant habitat 

will at some point become inhabited by fish due to natural recruitment (straying). 

Since stray rates are generally low for salmon (~1%) and the current population size 

is small, straying to colonize a new area is unlikely. However, this strategy should 

be employed for two reasons: First, populations started by naturally colonization may 

be more likely to succeed than by stocking and second, leaving some quality habitat 

vacant for natural recruitment provides a source of comparison for passive 

management areas. Monitor these reaches by juvenile assessment and redd 

surveys on an annual basis. 

12.1.7 Monitor 2008 redds to evaluate spawning success (YOY) 

Develop a plan to assess natural reproduction by 2008 spawners for relative 

abundance and spatial distribution before sampling season. Consider alternative 

sampling (e.g. snorkeling) if early sampling is desired. State the objectives of the 

sampling and consider information that will be needed for adaptive management. 

Target reaches known to have had spawning or adult escapement in 2008 should be 

sampled. Also, sampling throughout the basin, with focus on areas that are not 

stocked with fry will help to describe the spatial distribution of reproduction. 

Assessment of natural reproduction is pivotal to understanding progress towards 

PRFP Page 37

estoration, and to effectively adjust management to optimize chances for 

restoration. 

12.1.8 Investigate recruitment from natural spawning relative to other 

enhancement strategies 

Fry stocking has generated high density juvenile salmon populations in some areas, 

but the net difference in production from fry stocking versus natural spawning is 

unknown. Options for optimal enhancement strategy for Maine Rivers can not be 

determined without these data. Natural spawning encompasses several life history 

components that are absent in the hatchery program (mate choice, spawning 

behavior, emergence, etc) and is the ultimate goal of restoration. 

12.2.1 Reducing sea-run broodstock needs with a goal of increasing sea-run 

adult escapement (e.g. alternative broodstock sources, reviewing production 

needs, evaluation hatchery production potential) 

This will require forming a team that will either be the same team that handles 

12.1.2, or works very closely with that team. The team will develop and review, 

under a risk-benefit framework, various approaches to achieve this task. The work 

must also be fully compatible with the BSMP and to achieve this task the GDAT will 

need to be closely involved. GDAT and Conservation Hatchery Action Team 

(CHAT) will also review and make final recommendations. 

12.3.1 Review methods and ideas for using precocious parr in addition to 

adults as broodstock 

This task will be covered under 12.1.2 with consultation with the CHAT, field, and 

hatchery staff. Further development will be required to make the concepts 

operational if and when additional life stages are to be used. 

12.4.1 Review the potential to rejuvenate kelts, and identify possible uses (e.g. 

broodstock, spawning escapement) 

This will require forming a team that will either be the same team that handles tasks 

12.1.2 and 12.2.1, or works very closely with those team(s). The team will develop 

and review the, cost-benefit of various approaches to achieve this task. The work 

must also be fully compatible with the BSMP and to achieve this task the GDAT will 

need to be closely involved. GDAT and CHAT will also review and make final 

recommendations. 

12.5.1 Collaborate with PPL, PRRT, and Federal Agencies to assess the Milford 

fish lift 

The capability of the proposed Milford fish lift to provide safe, timely, and effective 

upstream fish passage for Atlantic salmon and other diadromous fish species must 

be confirmed. Once the lift is operational, MDMR will work with PPL, federal 

agencies, and the PRRT to evaluate the lift for passage effectiveness for adult 

salmon. It is our hope that MDMR will be able to use the Veazie Dam fishway trap 

as a collection point to mark and tag Atlantic salmon during the first year of the lift’s 

evaluation (prior to removal of the Veazie Dam). 

PRFP Page 38

12.6.1 Proposal to investigate natural spawning performance of translocated 

adult salmon 

Natural spawning is fundamental to restoring self-sustaining populations, and few 

management actions in the Penobscot promote natural spawning. Escapement to 

headwater spawning habitat is compromised by upstream passage deficiencies and 

other factors (e.g. imprinting). The reproductive success of adult sea-run salmon 

transported directly into spawning habitat will be assessed. The effectiveness of 

natural spawning relative to other enhancement techniques (e.g. fry stocking) will be 

assessed (Task 12.1.8). 

13.1.1 Literature review evaluating causes and remedies for poor performance 

of hatchery fry relative to wild fry 

Survival of hatchery reared juveniles is low relative to naturally reared fish. Although 

the mechanism for post release mortality is often not well described, physical and 

behavioral deficiencies in hatchery fish that may contribute to poor survival are well 

documented. Emerging techniques in the science of reintroduction biology (e.g., 

environmental conditioning, life-skills training) offer high potential for improved 

performance, often at minimal cost. Increasing performance of stocked fish may be 

more cost effective than increasing production of stocked fish as a mechanism for 

increasing adult returns. These techniques will be examined for applicability to the 

Maine salmon program. 

13.1.2 Literature review evaluating causes and remedies for poor performance 

of hatchery smolts relative to wild smolts 

Survival of hatchery-reared juveniles is low relative to naturally reared fish. Although 

the mechanism for post release mortality is often not well described, physical and 

behavioral deficiencies in hatchery fish which may contribute to poor survival are 

well documented. Techniques in the science of reintroduction biology (e.g. 

environmental conditioning, life-skills training, stocking at night) have the potential to 

improve hatchery-reared smolt performance. Increasing performance of stocked fish 

may be more cost effective than increasing production of stocked fish as a 

mechanism for increasing adult returns. These techniques will be examined for 

applicability to the Maine salmon program. 

13.2.1 Develop an integrated stock enhancement program to optimize adult 

Atlantic salmon returns 

The objective is to consider when, where, and how each life stage is stocked in 

order to maximize their accumulative contributions to adult returns and evaluate the 

efficacy of stocking. It is critical that we are able to evaluate the contributions of 

each hatchery product to juvenile production and adult returns. This will require a 

stocking program that allows for the evaluation of individual stocking strategies 

(Appendix D fry, GLNFH parr, adults, smolts). Future allocations of hatchery-reared 

products should consider current data; modeled population viability (Appendix B), 

potential productivity (Appendix C and Task 13.3.3), logistical constraints, and 

stocking of other salmon life stages (Task 13.2.2). The plan should review existing 

PRFP Page 39

strategies, and integrate and complement other enhancement strategy comparisons 

(i.e. Dennys River fry entirely point stocked; Kennebec’s River primary strategy is 

egg planting; Narraguagus River hatchery-reared smolts but no parr; Sheepscot and 

Narraguagus Rivers 0+ hatchery-reared parr). This integrated stocking plan will be 

developed concurrently with the adaptive management and assessment plans. 

13.2.2 Develop and implement an integrated assessment plan 

Atlantic salmon population assessment may include capturing emerging alevin, 0+ 

and older stream resident juveniles, emigrating smolts, and immigrating adults. Less 

invasive counts may be made by observing juveniles and adults during snorkel 

surveying, adults on video or using PIT or ultrasonic tag technology, and locating 

redds in spawning habitat. Each assessment method provides different information, 

which can be integrated to estimate vital rates (e.g. survival, growth, movement) for 

individuals or cohorts and/or compare relative abundance among sites, subwatersheds, 

and years. Sampling populations in natural systems requires an 

unbiased and spatially distributed sampling approach that balances data collections 

for temporal population trends and status, and evaluating management actions 

(Appendix H). The plan will rely primarily on Catch-Per-Unit-Effort (CPUE) 

electrofishing protocol for stream resident juveniles. An approach integrating CPUE 

with the few long term salmon population assessment sites allows sampling more 

sites in sub-drainages and provides a broad index of population abundance and 

distribution. The assessment plan will rely on interim life stage measures, but must 

ultimately integrate the results to estimate population growth parameters or lifetime 

reproductive success. Sampling methodology will be standardized to assist in 

comparisons between/within sub-drainages. All targeted research projects will 

include rigorous experimental designs developed through the proposal process and 

peer review (e.g. CHAT). 

13.2.3 Develop and implement a standardized juvenile assessment scheme 

Assessment of juvenile population status and trends requires an unbiased and 

representative sample (see Appendix H, Task 13.2.2). Sampling should consider for 

trend and status analysis. In addition, sampling should allow for greater effort 

depending on the assessment needs of biologists and managers. Finally, sampling 

must be flexible to allow un-sampled sites to be accounted for, and to add sites as 

needed. Collecting data under an integrated probabilistic sampling plan with 

standardized protocols should increase statistical power, focus sampling efforts, and 

allow analysis at various spatial and temporal scales. The sampling plan for the 

Penobscot will be the core for a larger state-wide sampling plan. The sampling plan 

could include both removal population estimates and CPUE methods, should be 

spatially balanced and accommodate varying sampling effort across space. When 

appropriate, field methods for research projects should conform to this standardized 

sampling scheme. 

13.2.4 Proposal to expand MDMR egg planting research into the Penobscot 

Egg planting provides one of the two most naturalistic approaches for introducing 

juvenile fish (along with adult stocking) to the environment. It also affords managers 

PRFP Page 40

the ability to target specific areas to introduce fish. Establishing an egg planting 

project that integrates with work already underway would allow a comparison 

between sea-run source eggs and eggs from captive reared adults (Penobscot F2). 

13.2.5 Develop a fry stocking adaptive management plan 

The goal of the plan is to maximize the number of smolts reaching Penobscot Bay 

from fry stocking (Appendix E). Adaptive management forces managers to clearly 

identify goals and assumptions, state management strategy, design monitoring, and 

recognize the links between expected outcome(s) and management changes. Fry 

have been stocked in the watershed since 1990 and resulted in high parr and smolt 

densities in some areas; however, adult returns and natural spawning from naturally 

reared salmon remain low. In addition to allocation decisions (i.e. location, density, 

method), the quality of the fry and the characteristics and conditions of the habitat 

also affects survival. Past decisions for the annual allocations of fry among and 

within sub-basins need to be documented (Task 13.2.2) and combined with data on 

river conditions (e.g., flow, temperature) and fry quality (e.g., development index 

(DI), relative size number/lb) to develop feedback to the hatchery on product survival 

(Task 13.2.7). Current practices will be reviewed and stocking strategies developed 

based on analysis of past experiences and use of models to aid in the selection of 

suitable habitats to stock with appropriate life stages. Allocations are currently 

based on biotic, abiotic, logistics, and observed results. Population viability and 

habitat productions models (Appendix B and C) may assist in identifying habitats 

that have suitable characteristics for salmon. 

13.2.6 Review and assess causes and remedies for poor natural recruitment 

In the Penobscot drainage, natural recruitment is limited, in part, because the 

numbers of wild spawners are adult returns is limited in part by inadequate to foster 

robust juvenile populations. It is therefore important to understand possible causes 

and work to remedy them. Increased adult escapement alone will not remedy poor 

juvenile recruitment if the habitat is compromised and limiting. 

13.2.7 Report: Juvenile production from fry stocking 

Fry stocking has been an integral management tool for conserving Atlantic salmon 

since 1990. To date there has been no review of the practice and its contributions to 

adult returns. An assessment of past practices (recent allocations and distribution 

procedures) and the relative contributions of this enhancement strategy to juvenile 

populations, smolt production, and it contributions to adult returns in is needed. 

13.2.8 Stock fry and assess according to existing management practices 

MDMR is currently reviewing stocking and population assessment practices to gain 

better information for adaptive management. Prior to the development of the 

integrated stock enhancement program, biologists will continue stock fry according 

to existing practices. 

13.2.9 Stock fry according to fry stocking adaptive management plan 

PRFP Page 41

This task is implementing the integrated enhancement plan (Task 13.2.1) and the fry 

stocking adaptive management plan (Task 13.2.5). Carefully documenting stocking 

methods, environmental conditions, and product characteristics (e.g. stocking 

density, release type, temperature flow, DI etc.) during stocking is required to allow 

feedback to the adaptive management of fry. 

13.2.10 Evaluate alternative fry stocking strategies/locations to increase smolt 

production 

Since stocking hatchery fry became one of the contemporary restoration strategies 

for the Maine salmon program, the approach has been to scatter fry in the mainstem 

of major tributaries to the Penobscot (e.g. Piscataquis, East Branch). While scatter 

stocking is more labor intensive than point stocking, it was adopted to reduce 

intraspecific competition. This strategy has produced high juvenile densities in some 

but not all of the areas currently stocked. By maintaining past strategies in some 

reaches, alternative strategies to increase juvenile production (parr and smolts) 

using can be tested using a Before-After/Control-Impact (BACI) design. Alternative 

strategies to test include, but may not be limited to: allocating a portion of fry stocked 

in mainstem reaches to smaller sized streams; stocking vacant tributaries (not being 

monitoring for natural re-colonization) in the lower sub watersheds where population 

viability may be higher than in headwaters above dams; and varying fry stocking 

densities annually at locations, to mimic natural spawning variability (e.g. high fall 

water levels – more spawning likely to occur in tributaries and farther upstream). To 

ensure effective assessment (Task 13.2.2), strategies will be segregated 

geographically. 

13.2.11 Develop a parr stocking adaptive management plan 

The goal of the plan is to maximum the number of smolt reaching Penobscot Bay 

from stocking parr (Appendix E). Parr are currently the by-product of the 

accelerated one-year smolt program at GLNFH. Past decisions for the annual 

allocations of GLNFH parr needs to be documented (Task 13.2.7). Future 

allocations need to considered: location relative to past experience and modeled 

population viability (Appendix B), potential productivity (Appendix C and Task 

13.3.3), and stocking of other salmon life stages. The potential to stock 0+ parr 

reared at ambient water temperatures also needs to be evaluated. Integrating smolt, 

parr, and fry stocking includes stocking parr in waters where fry perform poorly (e.g. 

wider rivers, high levels of predators/competitors) or where insufficient fry numbers 

are available to stock, and segregating parr from smolt stocking. The plan should 

allocate parr into reaches with sufficient quality habitat for the typical number of parr 

produced by GLNFH to survive for 8 to 32 months in the fresh water environment. 

Resulting parr densities will depend in part on the size or physiological state of the 

fish when stocked. Current data on the proportion of the stocked parr that smolt the 

following spring (P8) suggests that most GLNFH parr emigrate after only one winter 

in the wild. In contrast, a large proportion of 0+ parr reared on ambient water at 

CBNFH spend two winters in freshwater (P20). The plan needs to anticipate 

changes in stocking strategy as more is learned about how size at stocking affects 

the proportion of smolts emigrating the spring after stocking and as adult returns 

PRFP Page 42

occur. Assessment is likely to include a mix of monitoring for stream resident 

juveniles, emigrating smolt, and documenting spawning activity. Reproductive 

success relative to other stocked life history stages and wild fish will also need to be 

assessed, and should be coupled with return rate to inform management decisions. 

13.2.12 Literature review evaluating causes and remedies for poor 

performance of hatchery parr relative to wild parr 

The current parr program for the Penobscot is a by-product of the smolt program. 

However, stocking 300K fall parr has the potential for large contributions to adult 

returns. What can be done to increase their survival? Is there differential marine 

survival for parr that spend one winter in fresh water versus two winters? What 

factors influence overwinter survival, smoltification and marine survival? 

13.2.13 Stock parr and assess according to existing management practices 

MDMR is currently refining stocking practices and population assessment practices 

to gain better information for adaptive management. Prior to this transition, parr 

stocking and assessment will continue according to current standard operating 

procedures (Appendix E). The stocking plan for 2009 will follow the same stocking 

regimes as 2008 (1/3 Piscataquis, 1/3 Pleasant, 1/6 below Howland, 1/6 below 

Great Works). For 2008, approximately 330,000 parr were stocked. All parr stocked 

in the Pleasant drainage (~130,000) received a left ventral and adipose fin clip. In 

2009, they will receive a left ventral clip. 

13.2.14 Stock parr according to parr stocking adaptive management plan 

This task is implementing the integrated enhancement plan (Task 13.2.1) and the 

parr stocking adaptive management plan (Task 13.2.11). 

13.2.15 Report current stocking practices (fry, parr, smolts, adults), 

documenting decisions for annual allocations for each life stage 

Fry, parr, and smolt stocking are the standard stock enhancement practices use in 

the Penobscot watershed. The contribution of hatchery smolt stocking to adult 

returns is well documented but the relative effectiveness of other enhancement 

methods is poorly characterized. Reporting on current decision making practices 

and documenting recent changes will provide the foundation for the adaptive 

management plan (Appendix D) and the integrated enhancement program (Task 

13.2.1). 

13.2.16 Assess hatchery product marking scheme 

In an effort to evaluate return rates for all hatchery products being stocked in the 

Penobscot, the existing marking scheme needs to be assessed. Currently, the adult 

return rates for unmarked smolts are overestimated due to misidentification of adult 

returns from unmarked parr. It is difficult to distinguish returns from unmarked parr 

that emigrate after one winter from unmarked smolts that emigrate the same spring. 

Any marking scheme will need to fit into the broader context of MDMR’s integrated 

assessment plan. 

PRFP Page 43

13.3.1 Review and develop habitat based productivity estimates, integrating 

fry and parr performance, habitat data, and water quality 

The seven sub-watersheds identified in the plan differ in accessibility to salmon 

(passage and connectivity), resident and introduced fish communities, 

geomorphology (thus interspersion and complexity of salmon habitat), hydrologic 

regime, thermal regime, underlying aquifers and bedrock, land use patterns, and 

base flow and storm flow water chemistry. These factors and others (e.g. stream 

depth and width, N:P ratio, alkalinity, conductivity, temperature, pH) affect habitat 

suitability for Atlantic salmon. The ability of these factors to predict juvenile habitat 

suitability and provide insight for management decisions will be assessed using 

existing information 

14.1.1 Evaluate smolt stocking strategies to minimize smolt mortality 

Stocking smolts directly into headwater spawning habitat would improve imprinting 

to that habitat, but would subject smolts to higher (35-37%) cumulative dam-related 

mortality relative to downriver releases and reduce the number of adult returns. Net 

spawning escapement to headwater habitat is further reduced (42-57%) due to 

upstream passage inefficiencies. An integrated approach to smolt stocking and 

adult translocation may increase net spawning escapement to headwater habitat by 

77-94% with no change in stocking numbers or marine survival. 

14.1.2 Proposal to evaluate environmental conditioning of smolts (freshwater 

smolt ponds and sea-cages) to improve survival during transition to the 

marine environment 

High mortality of Penobscot smolts occurs during transition to the marine 

environment (~50% mortality, NOAA Fisheries, unpublished data), and seems higher 

for hatchery-reared than wild smolts. Increases in marine survival have been 

demonstrated elsewhere by acclimating hatchery-reared smolts to the marine 

environment in sea-cages prior to release. Staging smolts in the West Enfield smolt 

ponds prior to sea-cage acclimation may enhance imprinting to the Penobscot River 

and improve adult return rates. 

14.1.3 Proposal to capture and captive rear in sea-cages wild and/or naturallyreared 

Penobscot smolts for release as sexually mature adults in selected 

river reaches 

This proposal investigates a strategy for circumventing in-river and ocean mortality 

by rearing wild and/or naturally-reared smolts in sea-cages to adults and releasing 

them in selected river reaches to spawn. The outcome has the potential to increase 

adult escapement and increase spawning effectiveness, two strategies that have 

been identified in our strategic plan. 

14.2.1 Develop a smolt stocking adaptive management plan 

The goal is to balance the number of smolts reaching Penobscot Bay (Appendix E) 

with their motivation to ascend the river to suitable spawning habitat as returning 

adults. In addition, smolt stocking will need to be responsive to broodstock 

requirements as outlined in the BSMP. Past decisions for the annual allocations of 

PRFP Page 44

smolts needs to be documented (Task 13.2.7). Future allocations need to consider: 

1) homing to suitable habitat, 2) survival due to migration through dams (Appendix 

H), 3) seasonal timing, 4) physiological timing, 5) stocking of other salmon life 

stages, and 6) broodstock targets. Rearing and release strategies (e.g. smolt 

ponds) that have the potential to improve smolt “quality” and survival need to be 

evaluated and tested. The return rate of marked smolts is the primary method for 

assessing the effectiveness of management actions. Reproductive success relative 

to other stocked life history stages and wild fish will also need to be assessed, and 

should be coupled with return rate to inform management decisions. 

14.2.2 Stock smolts and assess according to existing management practices 

MDMR is currently refining stocking and assessment practices to improve adaptive 

management. Prior to these transitions, smolt stocking and assessment will 

continue according to current standard operating procedures (Appendix E). The 

stocking plan for 2009 will follow the same stocking regimes as 2007 and 2008. 

~ 175,000 tagged PN stocked above the Veazie Dam (Morin Fuel) 

~ 200,000 PN stocked in the Pleasant River (Milo) 

~ 200,000 PN stocked at Passadumkeag boat launch (mainstem Penobscot) 

~ 25,000 PN stocked into West Enfield smolt ponds 

14.2.3 Stock smolts according to smolt stocking adaptive management plan 

Once the stocking adaptive management plan (Task 14.2.1) has been developed, 

smolt will be stocked accordingly. 

14.3.1 Proposal to evaluate downstream smolt passage efficiency in the 

Piscataquis River 

The Upper Piscataquis River contains over 3,000 units of the most productive 

Atlantic salmon habitat in the Penobscot watershed. Safe downstream passage for 

migrating smolts is essential for restoration of this critical habitat, but downstream 

passage efficiency data are lacking for Piscataquis River dams (except Howland 

Dam which is scheduled to be bypassed as part of the PRRP). Downstream 

passage efficiency data are required to confirm adequate downstream passage, or 

to identify and correct deficiencies at the Guilford Industries, Moosehead 

Manufacturing, and Browns Mill dams. 

14.3.2 Collaborate with PRRT to test downstream passage measures (e.g. 

manipulate operating regimes) at PRRT owned dams prior to dam removal 

MDMR would like to capitalize on a unique opportunity to investigate operating 

regimes at hydro-electric dams to enhance downstream fish passage efficiency. 

Modifications to operating regimes with potential to improve downstream passage 

efficiency will be identified and tested. Techniques that prove effective will be 

applied at hydro-power facilities that are not scheduled for removal to improve 

downstream passage and survival of migrating salmon. 

15.1.1 Assess feasibility of increasing or reallocating hatchery smolt 

production to produce more adult returns 

PRFP Page 45

One strategy to increase adult returns is to increase the numbers of smolt being 

stocked. Smolts have the highest adult return rates for any hatchery product 

currently being produced. It stands to reason that if you convert fry to smolt you can 

increase adult returns without the need for additional broodstock. While this sounds 

simple, it would require a reorganization of hatchery operations and additional 

capital. 

References 

DMR (Dept. Marine Resources) and IFW (Dept. Inland Fish and Wildlife). 2008. 

Strategic Plan for the Restoration of Diadromous Fishes to the Penobscot River. 

Fay, C., M. Barton, S. Craig, A. Hecht, J. Pruden, R. Saunders, T. Sheehan, and 

J.Trial. 2006. Status review for anadromous Atlantic salmon (Salmo salar) in the 

United States. Report to the National Marine Fisheries Service and the U.S. Fish 

and Wildlife Service. 294 pp. 

NRC (National Research Council), USA. 2004. Atlantic salmon in Maine: A 

challenge in conservation and ecosystem management. Final report from the 

committee on Atlantic salmon in Maine. National Academy Press, Washington, 

DC. 62 pp. 

SEI (Sustainable Ecosystem Institute). 2007. Review of Atlantic salmon hatchery 

protocols, production, and product assessment. Sustainable Ecosystem Institute, 

Portland OR. 91 pp. 

Wright J., J Sweka, A. Abbott, and T Trinko. 2008. GIS-based Atlantic salmon 

habitat model, draft, Appendix C. In Biological valuation of Atlantic salmon 

habitat within the Gulf of Maine distinct population segment. National Marine 

Fisheries Service, Gloucester, MA. 

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Section 2 - Passage and Connectivity 

PRFP Page 47

Authors: Norm Dubé and Gail Wippelhauser 

Introduction 

The National Research Council (NRC 2004) listed dams as a major threat to Atlantic 

salmon populations since dams prevent or impede upstream and downstream fish 

migrations and alter or destroy habitat. The Strategic Plan for the Restoration of 

Diadromous Fishes to the Penobscot River also listed dams as a major contributor 

to the decline of many fish species in the Penobscot River. 

Whereas effects of structures such as dams upon diadromous fish species are fairly 

evident, there are other structures that may appear innocuous to diadromous fish at 

first glance but may not be in the long term. Road crossings may seasonally be an 

impediment to instream fish movements or prevent movement altogether. For 

example, hanging culverts may prevent juvenile salmon from reaching summer 

refugia and bridges whose abutments are narrower than the stream width form a 

pinch point causing hydraulic barriers to the upstream movements of weaker 

swimming diadromous species such as smelt. In order to obtain recovery of the 

target diadromous fish species in the Penobscot River, affects upon inriver 

migrations and movements by the various life stages of a the target species needs 

to be as benign as possible. 

There are 14 hydroelectric projects located on the mainstem Penobscot River and its 

major tributaries (Table 8). Of these, nine hydro projects have been issued licenses 

by the Federal Energy Regulatory Commission (FERC) and five smaller projects 

have been issued license exemptions. In addition, one project never completed 

installation of generating equipment and was never granted a license or exemption 

(Guilford); one dam (Matagamon) was deemed non-jurisdictional by FERC because 

of the lack of headwater benefits to downstream hydro generation; and one project 

surrendered its license exemption (West Winterport) in anticipation of project 

removal. 

There are several avenues available to improve or correct passage problems. The 

most obvious remedy is removal of the impediment but this strategy is best suited to 

small barriers at this time. However, removal of the first (Veazie) and second (Great 

Works) dams on the lower mainstem Penobscot River and installation of an 

innovative natural bypass around the first dam (Howland) on the lower Piscataquis 

River as part of the unprecedented Penobscot River Restoration Project has the 

potential to radically decrease upstream and downstream passage effects on 

migrating fish. 

One strategy allowing fish to migrate around hydro projects is to install upstream and 

downstream fish passage facilities. All the major dams in the Penobscot River 

drainage (exclusive of the West Branch, Penobscot River) currently have upstream 

fish passage facilities (Table 9). Most of the upstream fish passage facilities were 

constructed in the 1960s and early 1970s as part of the early restoration program for 

PRFP Page 48

Atlantic salmon. Two dams on the Stillwater Branch (Orono, Stillwater) do not have 

upstream fish passage facilities but upstream passage could be installed at a later 

date pending studies of fish attraction to the Orono project tailrace. Two small hydro 

projects on the Sebec River do not have upstream fish passage facilities primarily 

Table 8. FERC licensed or exempted hydroelectric projects and associated dams, Penobscot River 

(exclusive of the West Branch, Penobscot River). 

Dates of License/Exemption 

Project (FERC No.) Water 1 

Capacity L, E 2 

Issuance Termination Amendment 

Veazie (2403) PN 8.4 MW L 04/20/1998 04/01/2038 04/28/2005 

Great Works (2312) PN 7.73 MW L 04/01/1962 03/31/2002 3 

12/28/1981 

Milford (2354) PN 6.4 MW 4 

L 04/20/1998 04/01/2038 04/18/2005 

West Enfield (2600) PN 13 MW L 06/26/1984 5 05/31/2024 07/15/1986; 

01/23/1989; 

06/04/1997; 

04/18/2005 

Mattaceunk (2520) PN 19.2 MW L 09/30/1988 08/31/2018 02/09/1990 

Orono (2710) STW 2.33 MW L 12/08/2005 6 11/30/2045 

Stillwater (2712) STW 1.95 MW L 04/20/1998 7 04/01/2038 04/28/2005 

Howland (2721) PQ 1.86 MW L 09/21/1980 09/30/2000 8 

Brown’s Mill (5613) PQ 0.55 MW E 9 

08/03/1982 - 

Moosehead (5912) PQ 0.3 MW E 06/02/1982 - 

Guilford (8316) 10 

PQ - - - - 

Milo (5647) SR 0.6 MW E 02/23/1982 - 

Sebec (7253) SR 0.49 MW E 09/26/1983 - 08/03/2006 

Lowell Tannery (4202) PD 0.95 MW L 10/31/1980 09/30/2023 

Matagamon (UL01-02) 11 

EBPN - - - - 

Frankfort (6618) MS 0.55MW E 09/20/1982 - 03/23/1995 

West Winterport MS 0.15 MW E 06/25/1982 06/28/2002 12 

04/25/1994; 

03/25/1996 

1 

PN = Penobscot River; STW = Stillwater Branch; PQ = Piscataquis River; SR = Sebec River; PD = Passadumkeag 

River; EBPN = East Branch, Penobscot River; MS = Marsh Stream 

2 L = License, E = Exemption 

3 Project has been operating on an annual license 

4 Licensee proposes to increase total capacity to 8.0 MW 

5 Original license issued February 3, 1970 with effective date of January 1, 1938 and termination date of December 31, 

1987 

6 

Original license issued November 10, 1977 with effective date of July 1, 1950 and termination date of December 31, 

1993; FERC order dated September 25, 1985 accelerated license expiration to date of order; project has operated on 

an annual license since license expiration; project operation terminated in 1996 when wooden penstocks failed; 

redeveloped project began generation in early 2009 

7 

Original license issued in 1978 with effective date of April 1, 1962 and termination date of December 31, 1993; project 

operated on annual license until issuance of new license 

8 

Original license issued September 21, 1980 with an effective date of April 1, 1960 and termination date September 30, 

2000; project has been operating on an annual license 

9 

License exemptions have no expiration date 

10 

Preliminary permit application filed August 2, 1984 but project was never completed 

11 

FERC order issued March 8, 2001 stating Grand Lake Matagamon is non-jurisdictional due to lack of benefits to 

downstream generation 

12 FERC approved license exemption surrender by order dated June 28, 2002 

PRFP Page 49

ecause there is little habitat of value for Atlantic salmon in the river. As the 

restoration of diadromous fish species other than for Atlantic salmon progresses, 

upstream passage facilities may need to be constructed at these projects to provide 

passage into suitable habitat. Finally, the West Winterport Dam does have a Denil 

fishway but it is currently inoperable due to wide fluctuations in headpond levels that 

have occurred since the project’s license exemption was surrendered and the 

project no longer generates hydro power. It should be noted that the project’s owner 

is currently seeking to have the dam removed allowing the river reach affected by 

the dam to return to natural conditions. 

Table 9. Upstream and downstream fish passage facilities, Penobscot River (exclusive of the West 

Branch, Penobscot River). 

Upstream Passage Downstream Passage 

Project Yes (Yr. Built) No Yes (Yr. Built) No 

Veazie X (1970) 1 X 5 

Great Works X (1968) 2 

X 5 

Milford X (1968) 2 X 5 

West Enfield X (1988) 1 

X (1988) 6 

Mattaceunk X (1939) 3 

Orono X X (2009) 6 

Stillwater X X 5 

Howland X (1965) 2 X 5 

Brown’s Mill X (1973) 2 X 5 

Moosehead X (1973) 2 X 

Guilford X 1972) 2 X 

Milo X X 

Sebec X X 

Lowell Tannery X (1985) 2 X (1985) 6 

Matagamon X (1942) 4 

Frankfort X (1982) 2 X 

West Winterport X X 

1 Vertical slot fishway 

2 Denil fishway 

3 Pool and weir fishway 

4 Submerged orifice fishway 

5 Hydro projects retrofitted with downstream passage facilities including guidance structures, fish behavior 

technologies, and project operational measures 

6 Dedicated downstream passage facilities constructed when hydro project was redeveloped 

Four of the mainstem hydro projects have been retrofitted with downstream fish 

passage facilities that consist of guidance structures, fish behavior technologies, 

and/or project operational measures used singly or in combination to guide fish 

around the projects (Table 9). The West Enfield Project has a dedicated 

downstream fish passage system that was specifically constructed at the time the 

project was redeveloped to pass diadromous fish around the project. 

PRFP Page 50 

X 5 

X

On the tributaries, the downstream fish passage system at Lowell Tannery was 

installed at the time when the project was constructed. The downstream passage 

system at the Stillwater Project was a retrofit and facilities at the redeveloped Orono 

Project will be installed during spring 2009. On the Piscataquis River, the Brown’s 

Mill and Howland projects have retrofitted downstream passage facilities. The 

remaining hydro projects do not have downstream passage facilities. 

A license from FERC is required to construct, operate, and maintain a non-federal 

hydroelectric project (see FERC 2004 for specific requirements). License terms are 

granted for a period of 30 – 50 years with FERC granting 30-year license terms for 

projects that propose little or no redevelopment, new construction, new capacity, or 

enhancement; 40-year terms for projects that propose moderate redevelopment, 

new construction, new capacity, or enhancement; and 50-year terms for projects that 

propose extensive redevelopment, new construction, new capacity, or enhancement. 

FERC typically attaches conditions (articles) to a license for the duration of the 

license term. For example, FERC may attach an article requiring the licensee to 

install, operate, and maintain fish passage facilities when deemed necessary by 

natural resource agencies. 

FERC may issue an exemption from licensing under certain circumstances (FERC 

2004). Small hydroelectric projects of 5 MW or less are eligible for a 5MW 

exemption. Exemptions are subject only to conditions attached to the exemption 

and exemptions do not expire. 

Unless there are specific conditions attached to a license or exemption, it could 

prove burdensome to require hydro dam owners/operators to install and operate 

upstream and downstream fish passage facilities. Some, but not all, FERC licenses 

contain a reopener clause allowing agencies the opportunity to reopen a license 

before license expiration providing an avenue for agencies to seek the installation, 

operation, and maintenance of fish passage facilities. 

A settlement agreement between various parties, the Lower Penobscot River 

Multiparty Settlement Agreement (MPA), contains several triggers, provisions, and 

schedules for installation and operation of fish passage facilities depending on 

specific courses of action as the Penobscot River Restoration Project moves 

forward. 

Upstream and downstream passage of Atlantic salmon at selected hydro projects 

has been studied over the past 20 years (Appendix I). Some studies have been 

specific deliverables of FERC license articles following installation of fish passage 

facilities (e.g. downstream passage at West Enfield) while other studies have been 

undertaken to obtain general knowledge of inriver movements for Atlantic salmon. 

The University of Maine and others have also studied Atlantic salmon movements 

within the river system. Passage for other anadromous fish species has not been 

studied at all. There have been a few studies undertaken at selected hydro projects 

following installation of passage facilities for the catadromous eel. 

PRFP Page 51

The basic approach to understanding passage and connectivity issues in the 

Penobscot River with respect to fish passage facilities (Objectives 16, 17, and 18) 

will be to review the FERC licenses, FERC license exemptions, the various studies 

undertaken in the Penobscot River, and information on recent advances in fish 

passage technology. Once this information has been scrutinized, study plans will be 

developed and implemented to fill in knowledge gaps and develop recommendations 

for additional passage studies and/or facilities as needed. 

Fish passage efficiency and fish passage effectiveness are terms frequently used 

interchangeably to describe the adequacy of fish passage facilities at hydro projects. 

Fish passage engineers typically regard the two as follows (Ben Rizzo, USFWS, 

pers. comm.): 1) Fish passage efficiency is a quantitative assessment of the 

adequacy of a specific fish passage facility at a project. Passage efficiency studies 

typically require telemetry studies and results are expressed as a percentage of the 

number of tagged fish recorded as passing the device being evaluated divided by 

the number of tagged fish detected and available to be passed in the immediate 

vicinity of the device; and 2) Passage effectiveness can be a qualitative or 

quantitative assessment and is a description of the relative success of fish passage 

at a project or a specific passage facility. For example, a hydro project could have a 

spillway and powerhouse tailrace channel side by side but have only a powerhouse 

fishway. The powerhouse fishway could have a high "passage efficiency" (passes a 

high number of fish present in the powerhouse tailrace), yet the project could have a 

low upstream "passage effectiveness" due to many fish being attracted to and 

becoming delayed and/or stranded in the spillway reach. 

Outlets at lake and pond outlets can be problematic for the emigration of clupeids 

and American eel if there is not sufficient spill at the time of downstream movement. 

Part of Objective 18 will be to understand conditions at lake outlets at critical 

passage times, to develop recommendations, and institute facilities or measures as 

needed for alleviating impediments. 

Objective 19 includes periodic inspection of fish passage facilities to ensure that 

passage effectiveness is maintained. If a site continues to be problematic, then 

consultation with the dam owner to improve the passage success would follow. At 

an especially problematic site, partnering with the dam owner to install a passage 

facility may become a necessity to meet target restoration goals. This latter scenario 

may be difficult to pursue depending upon FERC license/license exemption 

conditions. 

Objective 20 seeks pathways to remedy smaller scale passage and/or connectivity 

impediments. Subtle instream connectivity conditions can be easily overlooked. 

Road-stream crossings can prove to be impassable at certain flows and at certain 

times of the year preventing instream movements of fish. For example, a culvert not 

properly embedded into the stream may not have sufficient flow in it to allow juvenile 

salmon access to cool water during critical summer periods. Likewise, beaver dams 

PRFP Page 52

can prevent the successful downstream movement of juvenile clupeids in late 

summer prior to early fall rains. 

There have been several initiatives in the Penobscot River watershed for surveying 

and cataloging small barriers and road-stream crossings. The USFWS was the lead 

agency in surveying the Kenduskeag Stream and Piscataquis River subwatershed 

(USFWS 2004a, 2004b). The Maine Forest Service surveyed small barriers and 

road-stream crossings in the lower Penobscot River from Orson Island in the 

mainstem Penobscot downstream to Fort Point in the Penobscot River estuary in 

2007 (MFS 2008) and the mid-Penobscot River tributaries (Piscataquis and 

Passadumkeag rivers) in 2008. Efforts to survey the remainder of the Penobscot 

River watershed is to continue as part of Objective 20. 

Municipalities, towns, and private landowners need to adopt policies and design 

guides to implement proper road construction and repair. The Maine Department of 

Transportation (MDOT) has developed the Waterway and Wildlife Crossing Policy 

and Design Guide to direct transportation planning, design, and construction while 

protecting aquatic and surface water resources (MDOT 2008). Other valuable 

resource documents for the design, placement, construction and permitting of roads. 

for the repair and maintenance of existing roads, for proper best management 

practices for the logging industry and small woodlot owners, and for assessment of 

fish passage needs include BMP Guidelines for Roads in Atlantic Salmon 

Watersheds (Project SHARE 2004), Best Management Practices for Forestry: 

Protecting Maine’s Water Quality (Maine Forest Service 2004), Maine Road-Stream 

Crossing Survey Manual (Abbott 2008), Design for Fish Passage at Roadway- 

Stream Crossings (Hotchkiss and Frei (2007),and Stream Simulation: An Ecological 

Approach to Providing Passage for Aquatic Organisms at Road-Stream Crossings 

(USDA Forest Service 2008) 

There have been numerous introductions (legal and illegal) of non-native fish 

species in the Penobscot River watershed with the most recent illegal introduction 

being northern pike in Pushaw Lake. Objective 21 employs several strategies to 

prevent further range expansion of non-native fish species. One approach to 

accomplish this goal includes the removal of undesirable fish species at fishway 

traps operated by MDMR. In order to achieve this strategy, a Memorandum of 

Understanding between the fisheries agencies needs to be completed so both 

agencies have a clear understanding of which species are to be removed from the 

river. Protocols for removing undesirable fish species also need to be developed to 

ensure proper procedures are followed once the MOU is executed. 

Risk assessments for determining the potential for range expansion on non-native 

fish species are be undertaken to inform the managers on how best to prevent the 

spread of invasive fish. Currently, there is a risk assessment group evaluating the 

potential impacts of the spread on northern pike into the mid and upper Penobscot 

River watershed. Recommendations of risk assessments could lead to structural 

PRFP Page 53

alteration of fish passage facilities or modification of their operation in some manner 

to prevent the upstream movement of undesirable species. 

Goal, Objectives, and Strategies 

Goal: Provide safe, timely, and effective upstream and downstream passage 

for diadromous fishes at barriers that restrict access between their historical 

habitats in the Penobscot basin. 

16.0 Objective: Increase upstream and downstream fish passage effectiveness 

at fish passage facilities at mainstem dams 14 within 10 years to ensure 

conservation spawning escapement of target restoration species and to 

ensure maximum emigration of target restoration species life stages 15 from 

freshwater habitats to the ocean. 

16.1 Measure: Improve upstream and downstream fish passage 

effectiveness at mainstem dams for juvenile and adult Atlantic salmon, 

alewife, American shad, and blueback herring within eight years. 

16.1.1 Strategy: Review FERC licenses and MPA 

16.1.2 Strategy: Review existing studies and information 

16.1.3 Strategy: Develop/conduct assessment studies to determine 

fish passage effectiveness and develop recommendations for 

fish passage improvements 

16.1.4 Strategy: Undertake fish passage improvements 

16.1.5 Strategy: Assess fish passage improvements 


effectiveness at mainstem dams for juvenile and adult American eel 

within 10 years of the removal of the Veazie and Great Works dams. 









at fish passage facilities at tributary dams 16 within 40 years to ensure 

conservation spawning escapement of target restoration species and to 

14 

Includes the Milford, West Enfield, and Mattaceunk dams on the mainstem Penobscot River and the Stillwater 

and Orono dams on the Stillwater Branch. 

15 

For example, Atlantic salmon smolts and kelts; juvenile and adult clupeids. 

16 

Howland, Browns Mill, Moosehead Manufacturing, Guilford, Lowell Tannery, and Frankfort dams 

PRFP Page 54

ensure maximum emigration of target restoration species life stages from 

freshwater habitats to the ocean. 


effectiveness at tributary dams for juvenile and adult Atlantic salmon 

within 10 years. 

17.1.1 Strategy: Review FERC licenses/exemptions and MPA 

17.1.2 Strategy: Review need/process to install/improve fish passage 

facilities at FERC non-jurisdictional dams 








effectiveness at the Howland and Lowell Tannery dams for juvenile 

and adult alewife within five years of stocking Phase 1 lakes located 

above these dams. 








effectiveness at Howland for juvenile and adult American shad and 

blueback herring within six years of stocking Group 1 habitat located 

above Howland. 

17.3.1 Strategy: Review FERC license and MPA 







effectiveness for juvenile and adult alewife, American shad, and 

blueback herring at remaining tributary dams within 40 years. 

17.4.1 Strategy: Review FERC licenses/exemptions 



PRFP Page 55







effectiveness for juvenile and adult American eel at Howland within 10 

years 

17.5.1 Strategy: Review FERC license and MPA 








effectiveness for juvenile and adult American eel at remaining tributary 

dams within 30 years. 

17.6.1 Strategy: Review FERC license exemptions 




17.6.4 Strategy: Use annual boat electrofishing survey results to 

determine fish passage requirements and installation timeline at 

remaining tributary dams 







at FERC non-jurisdictional dams within 20 years and lake and pond outlets 

within 50 years to ensure conservation spawning escapement of target 

restoration species and to ensure maximum emigration of target restoration 

species life stages from freshwater habitats to the ocean. 


effectiveness for Atlantic salmon at Grand Lake Matagamon within 20 

years. 


facilities at Grand Lake Matagamon Dam 

PRFP Page 56







effectiveness for alewife and American eels at lake and pond outlets 

within 50 years. 


facilities at lake and pond outlets 






19.0 Objective: Ensure proper operation of upstream and downstream fish 

passage facilities throughout the fish passage season (annually). 

19.1 Measure: Annually monitor upstream and downstream fish passage 

facilities operation to ensure the facilities are performing effectively. 

19.1.1 Strategy: Establish upstream and downstream fish passage 

facility operating protocols 

19.1.2 Strategy: Periodically inspect fish passage facilities during the 

fish passage season 

19.1.3 Strategy: Consult with owners of fish passage facilities 

regarding fish passage issues 

19.1.4 Strategy: Consult and/or partner with owners of fish passage 

facilities to improve effectiveness of fish passage facilities 

and/or fish passage measures. 

19.1.5 Strategy: Consult and/or partner with dam owners to install fish 

passage facilities at problematic passage sites. 

19.1.6 Strategy: Develop fish handling and trap operating protocols for 

the Milford Dam fish lift 

20.0 Objective: Increase stream connectivity at non-hydro dams, small barriers, 

culverts, hydraulic and physiological blocks, etc. within 50 years to ensure 

conservation spawning escapement and maximum emigration of target 

restoration species life stages, and to promote unimpeded instream 

movements of target restoration species life stages. 

20.1 Measure: Ensure that stream connectivity limitations are prevented or 

remediated. 

PRFP Page 57

20.1.1 Strategy: Monitor stream connectivity to ensure effective 

upstream and downstream fish passage and instream 

movements. 

20.1.2 Strategy: Consult with the Maine Department of Transportation 

(MDOT), cities and towns, and private landowners to ensure 

implementation of MDOT’s Waterway and Wildlife Crossing 

Policy and Design Guide at road crossings slated for 

replacement. 

20.1.3 Strategy: Identify road crossings and small barriers and 

prioritize passage needs by site and species. 

20.1.4 Strategy: Obtain funding to replace or remove problematic road 

crossing structures and remove critical barriers 

20.1.5 Strategy: Coordinate with other state and federal agencies and 

NGOs to use a standard protocol and tracking database 

20.1.6 Strategy: Encourage creation and funding of a Barrier Removal 

Program in the State of Maine. 

20.1.7 Strategy: Collaborate with resource agencies, lake associations, 

NGOs, etc. to resolve fish passage issues. 

20.1.8 Strategy: Research and implement alternative methods for 

habitat access. 

20.1.9 Strategy: Undertake with other resource agencies risk 

assessments of range expansion for undesirable fish species 

20.2 Measure: Improve stream connectivity limitations for juvenile and adult 

Atlantic salmon within 10 years. 

20.2.1 Strategy: Complete ongoing Penobscot watershed road 

crossing and small barrier survey 

20.2.2 Strategy: Determine stream connectivity limitations for juvenile 

and adult Atlantic salmon 

20.2.3 Strategy: Undertake stream connectivity improvements for 

Atlantic salmon 

20.3 Measure: Improve stream connectivity limitations for juvenile and adult 

alewife and American eel within 50 years 

20.3.1 Strategy: Determine stream connectivity limitations juvenile and 

adult alewife and American eel 

20.3.2 Strategy: Undertake stream connectivity improvements for 

alewife and American eel 

21.0 Objective: Restrict upstream passage of undesirable fish species at fish 

passage facilities. 

21.1 Measure: Develop agreements with resource agencies and fish 

passage facility operators to remove or prevent upstream movements 

of non-native and undesirable fish species at fish passage facilities 

within three years. 

PRFP Page 58

21.1.1 Strategy: Develop a Memorandum of Understanding (MOU) 

with the Maine Department of Inland Fisheries and Wildlife 

(MDIFW) for selectively removing non-native and undesirable 

fish species at the Veazie fishway trap and other fish passage 

facility trapping locations (e.g. Mattaceunk Dam) prior to the 

removal of Veazie and Great Works dams and installation of the 

Howland bypass. 

21.1.2 Strategy: Develop a Memorandum of Understanding (MOU) 

with the Maine Department of Inland Fisheries and Wildlife 

(MDIFW) for selectively removing non-native and undesirable 

fish species at the Milford fish lift fish sorting facility (post Veazie 

and Great Works dam removal) 

21.1.3 Strategy: Establish list, protocols, and measures for removing or 

allowing passage of non-native and undesirable fish species at 

fishway trapping locations 

21.1.4 Strategy: Undertake with other resource agencies risk 

assessments of range expansion for undesirable fish species 

21.1.5 Strategy: Develop Memorandum of Understandings with 

resource agencies and fish passage facility operators to prevent 

upstream movements of non-native/undesirable fish species at 

fish passage facilities 

21.2 Measure: Modify fish passage facilities to prevent upstream movement 

of undesirable fish species 

21.2.1 Strategy: Assess with other resource agencies physical and/or 

temporal modifications to fish passage facility operations that 

may selectively restrict passage of undesirable fish species prior 

to the removal of Veazie and Great Works and installation of the 

Howland bypass. 

21.2.2 Strategy: Obtain funding to structurally modify fish passage 

facilities 


The budget includes funding for two full-time Biologists, two full time Biology 

Specialists and two seasonal Conservation Aides. Budget is estimated for 2010- 

2014. 


16.1.1 

16.1.2 

Review FERC licenses and Lower 

Penobscot River Multiparty 

Settlement Agreement (MPA) for 

specific fish passage deliverables April-10 MDMR $7,710 

Review existing fish passage studies 

and migration/ movement studies for 

adult and juvenile Atlantic salmon April-10 MDMR $7,710 

PRFP Page 59

16.1.3 

16.1.4 

16.1.5 

16.2.1 

16.2.2 

16.2.3 

16.2.4 

16.2.5 

17.1.1 

17.1.2 

17.1.3 

17.1.4 

17.1.5 

Develop assessment study plans, 

conduct fish passage efficiency 

studies, and develop 

recommendations for fish passage 

improvements Dec. 2018 

Complete fish passage 

improvements based on passage 

efficiency studies Dec. 2020 

MDMR, USFWS, 

NOAA, Hydro 

Operators $185,040 

Hydro Operators, 

USFWS, NOAA, 

MDMR $15,420 

Assess fish passage facility 

MDMR, USFWS, 

NOAA, Hydro 

improvements 



Dec. 2023 Operators $185,040 

Settlement Agreement for specific 

Included in 

fish passage deliverables 


for juvenile and adult American eel 

undertaken within the Penobscot 

April-10 MDMR 

16.1.1 

River watershed 


April-10 MDMR $1,950 



MDMR, USFWS, 


NOAA, Hydro 

improvements 

April-22 Operators $92,520 

Complete fish passage facility 




improvements Dec. 2027 

Review FERC licenses, FERC 

license exemptions, and Lower 


Settlement Agreement for specific 

fish passage deliverables April-10 MDMR 


USFWS, NOAA, 

MDMR $15,420 

MDMR, USFWS, 

NOAA, Hydro 

Operators $92,520 

Included in 

16.1.1 

Review need and process to 

increase upstream and downstream 

fish passage efficiency at FERC nonjurisdictional 

dams located on 

tributaries April-10 MDMR $1,950 


and migration/ movement studies for 

adult and juvenile Atlantic salmon April-10 MDMR 





improvements December-20 




Included in 

16.1.2 

MDMR, USFWS, 

NOAA, Hydro 

Operators, Dam 

Owners $185,040 


Dam Owners, 

USFWS, NOAA, 

MDMR $15,420 

PRFP Page 60

17.1.6 

17.2.1 

17.2.2 

17.2.3 

17.2.4 

17.3.1 

17.3.2 

17.3.3 

17.3.4 

17.4.1 

17.4.2 


MDMR, USFWS, 

NOAA, Hydro 


improvements 




Dec. 2025 Owners $185,040 

specific fish passage deliverables at 

Included in 

Howland and Lowell Tannery 



April-10 MDMR 

16.1.1 


MDMR, USFWS, 


NOAA, Hydro 

improvements at Howland and 


Lowell Tannery December-20 Owners $46,260 



efficiency studies at Howland and 

Lowell Tannery Dec. 2022 


improvements at Howland and 

Lowell Tannery Dec. 2025 

Review FERC license and Lower 




Howland April-10 MDMR 





improvements December-20 



efficiency studies December-22 


Dam Owners, 

USFWS, NOAA, 

MDMR $7,710 

MDMR, USFWS, 

NOAA, Hydro 


Owners $46,260 

Included in 

16.1.1 

MDMR, USFWS, 

NOAA, Hydro 

Operator, Dam 

Owner $7,710 

Hydro Operator, 

Dam Owner, 

USFWS, NOAA, 

MDMR $3,855 


MDMR, USFWS, 

NOAA, Hydro 


improvements 

Review FERC licenses and FERC 

license exemptions for specific fish 

December-25 Owner $7,710 

passage deliverables at remaining 

Included in 

tributary dams 



April-10 MDMR 

16.1.1 

fish passage efficiency at FERC non- 

Included in 

jurisdictional dams April-10 MDMR 

17.1.2 

PRFP Page 61

17.4.3 

17.4.4 

17.4.5 

17.5.1 

17.5.2 

17.5.3 

17.5.4 

17.5.5 

17.6.1 

17.6.2 

17.6.3 

17.6.4 





improvements at remaining tributary 

dams December-45 




MDMR, USFWS, 

NOAA, Hydro 


Owners $185,040 


Dam Owners, 

USFWS, NOAA, 

MDMR $15,420 


MDMR, USFWS, 

NOAA, Hydro 


improvements 

Review FERC license and Lower 





Included in 

Howland 



April-10 MDMR 

16.1.1 


Included in 

River watershed 


April-10 MDMR 

16.2.2 


MDMR, USFWS, 


NOAA, Hydro 



improvements at Howland December-15 Owner $7,710 





Dam Owner, 

USFWS, NOAA, 

MDMR $3,855 


MDMR, USFWS, 

NOAA, Hydro 


improvements 

Review FERC licenses and FERC 

license exemptions for specific fish 


passage deliverables at remaining 

Included in 




April-10 MDMR 

16.1.1 


Included in 

jurisdictional dams 



April-10 MDMR 

17.1.2 


Included in 

River watershed April-10 MDMR 

16.2.2 

Utilize annual boat electrofishing 

surveys to determine requirement 

and assessment timeline for fish 

passage facilities at remaining Annually 

MDMR, MDIFW, 

USFWS, NOAA $2,500,000 

PRFP Page 62

17.6.5 

17.6.6 

17.6.7 

18.1.1 

18.1.2 

18.1.3 

18.1.4 

18.2.1 

18.2.2 

18.2.3 

18.2.4 






improvements at remaining tributary 

dams December-35 




MDMR, USFWS, 

NOAA, Hydro 


Owner $92,520 


Dam Owners, 

USFWS, NOAA, 

MDMR $15,420 


MDMR, USFWS, 

NOAA, Hydro 


improvements 





jurisdictional dams at lake and pond 

Included in 

outlets 




April-10 MDMR 

17.1.2 

recommendations for upstream and 

MDMR, USFWS, 

downstream fish passage at the 

NOAA, Dam 

Grand Lake Matagamon Dam December-25 Owner $15,420 





improvements at Grand Lake 

Matagamon December-30 



fish passage efficiency at lake and 

pond outlets April-10 MDMR 




recommendations for upstream and 

downstream fish passage at lake and 

pond outlets December-55 





improvements at lake and pond 

outlets December-60 

Dam Owner, 

USFWS, NOAA 

MDMR $7,710 

MDMR, USFWS, 

NOAA, Dam 

Owner $15,420 

Included in 

17.1.2 

MDMR, USFWS, 

NOAA, Dam 


Dam Owners, 

USFWS, NOAA, 

MDMR $30,840 

MDMR, USFWS, 

NOAA, Dam 


PRFP Page 63

19.1.1 

19.1.2 

19.1.3 

19.1.4 

19.1.5 

19.1.6 

20.1.1 

20.1.2 

20.1.3 

20.1.4 

20.1.5 

Review need to establish upstream 

and downstream fish passage facility 

operating protocols to ensure proper 

operation of upstream and 

downstream fish passage facilities April-10 MDMR $3,855 

Periodically inspect upstream and 

downstream fish passage facilities to 

ensure proper operation 

Consult with owners of fish passage 

facilities regarding fish passage 

issues As needed 

Consult and/or partner with owners 

of fish passage facilities to improve 

effectiveness of fish passage 

facilities and/or fish passage 

measures As needed 

Consult and/or partner with dam 

owners to install fish passage 

facilities at problematic passage sites As needed 

Develop fish handling and trap 

operating protocols for the Milford 

Dam fish lift April-10 

Monitor stream connectivity to 

ensure effective upstream and 

downstream fish passage and 

instream movements Annually 

Ensure implementation of the Maine 

Department of Transportation’s 

Waterway and Wildlife Crossing 

Policy and Design Guide 

Weekly during 

migration window MDMR, MDIFW $925,060 

Interagency 

Meetings 

Identify road crossings and small 

barriers and prioritize passage needs 

by site and fish species December-14 

Obtain funding to replace or remove 

problematic road crossing structures 

and to remove critical barriers Annually 

Coordinate with other state and 

federal agencies and NGOs to use a 

standard protocol and tracking 

database Annually 

MDMR, MDIFW, 

USFWS, NOAA, 


Dam Owners $115,630 

MDMR, MDIFW, 

USFWS, NOAA, 


Dam Owner $115,630 

MDMR, MDIFW, 

USFWS, NOAA, 


Dam Owner $115,630 

MDMR, MDIFW, 

USFWS, NOAA, 

PPL $15,420 

MDMR, MDIFW, 

MDEP, LURC, 

MFS, MDOT, 

USFWS, NOAA $115,630 

MDMR, MDOT, 

Cities, Towns, 

Land Owners $115,630 

MDMR, MFS, 

MDOT, MDIFW, 

USFWS, NOAA, 

Barrier Owners, 


MDMR, MFS, 

MDOT, USFWS, 

NOAA, Barrier 

Owners, Land 

Owners $231,260 

MDMR, MFS, 

MDOT, SPO, 

MDIFW, MDEP, 

LURC, USFWS, 

NOAA $96,360 

PRFP Page 64

20.1.6 

20.1.7 

20.1.8 

20.1.9 

20.2.1 

20.2.2 

20.2.3 

20.3.1 

20.3.2 

21.1.1 

Encourage creation and funding of a 

barrier removal program in the State 

of Maine April-11 

Collaborate with regulatory and 

resource agencies, lake 

associations, NGOs, etc. to resolve 

fish passage issues Annually 

Research and implement alternative 

methods for habitat access Annually 

Undertake with other resource 

agencies risk assessments of range 

expansion for non-native/undesirable 

fish species due to increased stream 

connectivity As needed 

Complete ongoing efforts to 

catalogue Penobscot River 

watershed road crossings and small 

barriers December-14 

Determine stream connectivity 

limitations for juvenile and adult 

Atlantic salmon April-12 

Undertake stream connectivity 

improvements for Atlantic salmon December-20 

Determine stream connectivity 

limitations for juvenile and adult 

alewife and American eel April-35 

Undertake stream connectivity 

improvements for juvenile and adult 

alewife and American eel December-60 

Develop a Memorandum of 

Understanding (MOU) with MDIFW 

for selectively removing nonnative/undesirable 

fish species at 

fishway passage trapping locations 

prior to removal of the Veazie and 

Great Works dams April-10 

MDMR, MFS, 

MDOT, SPO, 

MDIFW, MDEP, 

LURC, USFWS, 

NOAA $15,420 

MDMR, MFS, 

MDOT, MDIFW, 

MDEP, LURC, 

USFWS, NOAA, 


Land Owners, 

NGOs $96,360 

MDMR, MDIFW, 

USFWS, NOAA 


Land Owners, 

NGOs $48,180 

MDMR, MDIFW, 

USFWS, NOAA 

See Task 

23.1.2 and 

23.1.3 

MDMR, MDIFW, 

MFS, MDOT, 

USFWS, NOAA, 



MDMR, USFWS, 

NOAA $15,420 


Land Owners, 

MDMR, MDOT, 


MDMR, MDOT, 

USFWS, NOAA, 



MDMR, MDOT, 

USFWS, NOAA, 



MDMR, MDIFW. 


PRFP Page 65

21.1.2 

21.1.3 

21.1.4 

21.1.5 

21.2.1 

21.2.2 

Develop a Memorandum of 

Understanding (MOU) with MDIFW 

for selectively removing nonnative/undesirable 

fish species at the 

Milford fish lift sorting facility April-11 

Establish list of nonnative/undesirable 

fish species and 

protocols for removing or allowing 

passage at fish passage facility 

trapping locations April-10 

Undertake with other resource 

agencies risk assessments of range 

expansion for non-native/undesirable 

fish species at fish passage facilities As needed 

Develop Memorandum of 

Understandings with resource 

agencies and fish passage facility 

operators to prevent upstream 

movements of nonnative/undesirable 

fish species at fish 

passage facilities As needed 

Assess with other resource agencies 

the need for physical and/or temporal 

modifications to fish passage 

facilities As needed 

Obtain funding to trap or 

seasonally/permanently modify fish 

passage facilities to prevent 

upstream movement of nonnative/undesirable 

fish species As needed 


MDMR, MDIFW. 


MDMR, MDIFW. 


MDMR, MDIFW, 

USFWS, NOAA 

See Task 

23.1.2 and 

23.1.3 

MDMR, MDIFW, 

USFWS, NOAA, 



MDMR, MDIFW, 

USFWS, NOAA, 


Dam Owners 

Tasks 

23.1.1.1, 

23.1.1.3 and 

23.1.1.3 

MDMR, MDIFW, 

USFWS, NOAA, 



16.1.1 Review FERC Licenses and Lower Penobscot River Multiparty 

Settlement Agreement (MPA) for Specific Fish Passage Deliverables for 

Atlantic Salmon, Alewife, American Shad, and Blueback Herring 

Hydro licenses issued for the mainstem Penobscot River dams need review to 

determine what articles, if any, were included by FERC that address fish passage. 

Similarly, the Lower Penobscot River Multiparty Settlement Agreement (MPA) 

contains specific language on fish passage provisions that could affect timelines 

listed in the work plan. Additionally, the MPA spells out specific fish passage 

strategies depending on whether the Veazie and Great Works dams are removed 

and the Howland Dam is bypassed as well as to which entity would be responsible 

for funding, installing, and operating the fish passage facilities. 

16.1.2 Review Existing Fish Passage Studies and Migration/Movement Studies 

Undertaken within the Penobscot River Watershed 

PRFP Page 66

Over the past 20 years, there have been several studies undertaken by hydro dam 

operators, University of Maine graduate students, the Maine Atlantic Salmon 

Commission, and others attempting to determine the efficiency of fish passage 

facilities for juvenile and adult Atlantic salmon and to understand inriver movements 

of adult and juvenile Atlantic salmon. Passage at mainstem dams and inriver 

movements/migrations for other anadromous fish species have not been studied in 

the Penobscot River. There is a need to synthesize the Atlantic salmon information 

to provide for baseline conditions and to inform future passage studies for Atlantic 

salmon. 

16.1.3 Develop Assessment Study Plans, Conduct Fish Passage Efficiency 

Studies, and Develop Recommendations for Fish Passage Improvements for 

Juvenile and Adult Atlantic Salmon, Alewife, American Shad, and Blueback 

Herring at Mainstem Dams 

Not all existing fish passage facilities and/or operational measures (e.g. cycling 

turbines, opening sluice gates, temporary shutdown of generation) have been 

assessed for the passage of juvenile and adult Atlantic salmon and none of the 

existing fish passage facilities have been assessed for the passage of juvenile and 

adult alewife, American shad, and blueback herring. Studies of existing fish 

passage facilities will need to be undertaken to further understand bottlenecks 

and/or poor performance of fish passage facilities to make them more effective in 

successfully passing Atlantic salmon adults, smolts, and kelts and juvenile and adult 

alewife, American shad, and blueback herring around mainstem hydro projects. Any 

newly constructed fish passage facilities will need to undergo rigorous testing to 

ensure they function properly and are effective in passing the target restoration fish 

species. All studies should be undertaken over the course of a minimum of three 

field seasons. 

16.1.4 Complete Fish Passage Improvements Based on Passage Efficiency 

Studies 

Once fish passage efficiency studies are complete, redesign of existing facilities, 

operational changes to the existing facilities, and/or installation of additional fish 

passage facilities are to be undertaken. 

16.1.5 Assess Fish Passage Improvements for Juvenile and Adult Atlantic 

Salmon, Alewife, American Shad, and Blueback Herring at Mainstem Dams 

A minimum of three field seasons are needed to verify that the improvements allow 

the fish passage facilities to meet efficiency goals for passage of adult and juvenile 

Atlantic salmon, alewife, American shad, and blueback herring. 


Settlement Agreement (MPA) for Specific Fish Passage Deliverables for 

American Eel 

Hydro licenses issued for the mainstem Penobscot River dams need review to 

determine what articles, if any, were included by FERC that address fish passage. 

Similarly, the Lower Penobscot River Multiparty Settlement Agreement (MPA) 

PRFP Page 67

contains specific language on fish passage provisions that could affect timelines 

listed in the work plan. Additionally, the MSA spells out specific fish passage 

strategies depending on whether the Veazie and Great Works dams are removed 

and the Howland Dam is bypassed as well as to which entity would be responsible 

for funding, installing, and operating the fish passage facilities. 

16.2.2 Review Existing Fish Passage Studies for Juvenile and Adult American 

Eel Undertaken within the Penobscot River Watershed 

Over the past few years, there have been several studies undertaken by hydro dam 

operators attempting to determine the efficiency of fish passage facilities for juvenile 

and adult American eel. There is a need to synthesize this information to provide for 

baseline conditions and to inform future passage studies for American eel. 



Juvenile and Adult American Eel at Mainstem Dams 

Upstream fish passage facilities have recently been installed at some mainstem 

dams specifically targeting American eel. Likewise, downstream passage facilities 

have been constructed at some but not all of the mainstem dams. Once the review 

outlined in 16.2.2 is complete, studies of existing fish passage facilities will need to 

be undertaken to further understand bottlenecks and/or poor performance of fish 

passage facilities to make them more effective in successfully passing juvenile and 

adult American eel around hydro projects. Any newly constructed fish passage 

facilities will need to undergo rigorous testing to ensure they function properly and 

are effective in passing American eel. All studies should be undertaken over the 

course of a minimum of three field seasons after the Veazie and Great Works dams 

are removed 


Studies 




16.2.5 Assess Fish Passage Improvements for Juvenile and Adult American 

Eel at Mainstem Dams 



American eel. 

17.1.1 Review FERC Licenses, FERC License Exemptions, and Lower 

Penobscot River Multiparty Settlement Agreement (MPA) for Specific Fish 

Passage Deliverables for Juvenile and Adult Atlantic Salmon at Tributary 

Dams 

Hydro licenses and license exemptions issued for dams located on Penobscot River 

tributaries need review to determine what articles, if any, were included by FERC 

PRFP Page 68

that address fish passage. Similarly, the MPA contains specific language on fish 

passage provisions that could affect timelines listed in the work plan. Additionally, 

the MPA spells out specific fish passage strategies depending on whether the 

Veazie and Great Works dams are removed and the Howland Dam is bypassed as 

well as to which entity would be responsible for funding, installing, and operating the 

fish passage facilities. 

17.1.2 Review Need and Process to Increase Upstream and Downstream Fish 

Passage Efficiency at FERC Non-Jurisdictional Dams Located on Tributaries 

for Juvenile and Adult Atlantic Salmon 

There is at least one FERC non-jurisdictional dam on Penobscot River tributaries, 

the Guilford Dam located on the Piscataquis River, which is critical for passage of 

target restoration fish species. How fish passage improvements are addressed at 

this dam needs to be explored to develop options and approaches to ensure fish 

passage facilities meet established goals. 

17.1.3 Review Existing Fish Passage Studies and Migration/Movement 

Undertaken within the Penobscot River Watershed for Juvenile and Adult 


Over the past 20 years, there have been several studies undertaken by hydro dam 

operators, University of Maine graduate students, the Maine Atlantic Salmon 

Commission, and others attempting to determine the efficiency of fish passage 

facilities for juvenile and adult Atlantic salmon and to understand inriver movements 

of adult and juvenile Atlantic salmon. Passage at tributary dams and inriver 

movements/migrations for other anadromous fish species have not been studied in 

Penobscot River tributaries. There is a need to synthesize the Atlantic salmon 

information to provide for baseline conditions and to inform future passage studies 

for Atlantic salmon. 



Juvenile and Adult Atlantic Salmon 

Not all existing fish passage facilities and/or operational measures (e.g. cycling 

turbines, opening sluice gates, temporary shutdown of generation) have been 

assessed for the passage of juvenile and adult Atlantic salmon. Studies of existing 

fish passage facilities will need to be undertaken to further understand bottlenecks 

and/or poor performance of existing fish passage facilities to make them more 

effective in successfully passing Atlantic salmon adults, smolts, and kelts around 

tributary hydro projects and non-hydro dams. Any newly constructed fish passage 

facilities, including the Howland nature-like bypass, will need to undergo rigorous 

testing to ensure they function properly and are effective in passing the target 

restoration fish species. All studies should be undertaken over the course of a 

minimum of three field seasons 


Studies 

PRFP Page 69





Salmon at Tributary Dams 



Atlantic salmon. 


Settlement Agreement (MPA) for Specific Fish Passage Deliverables at 

Howland and Lowell Tannery for Juvenile and Adult Alewife 

Hydro licenses issued for the Howland and Lowell Tannery dams located on 

Penobscot River tributaries need review to determine what articles, if any, were 

included by FERC that address fish passage. Similarly, the MPA contains specific 

language on fish passage provisions that could affect timelines listed in the work 

plan. Additionally, the MPA spells out specific fish passage strategies depending on 

whether the Veazie and Great Works dams are removed and the Howland Dam is 

bypassed as well as to which entity would be responsible for funding, installing, and 

operating the fish passage facilities. 



Juvenile and Adult Alewife 

The Howland and Lowell Tannery fish passage facilities, installed in 1965 (Howland) 

and 1985 (Lowell Tannery), have not been assessed for the passage of juvenile and 

adult alewife since they were primarily constructed for passage of Atlantic salmon. 

Studies of the existing upstream and downstream fish passage facilities and/or 

operational measures (e.g. cycling turbines, opening sluice gates, temporary 

shutdown of generation) need to be undertaken to ensure the existing passage 

facilities function properly and are effective in passing alewife. Any newly 

constructed fish passage facilities (e.g. Howland bypass) will need to undergo 

rigorous testing to ensure they function properly and are effective in passing alewife. 

All studies should be undertaken over the course of a minimum of three field 

seasons after Phase 1 lakes located above the Howland and Lowell Tannery dams 

are stocked. 


Studies 

Once fish passage efficiency studies are complete, redesign of existing facilities at 

Lowell Tannery and Howland including the bypass, operational changes to the 

existing facilities or bypass, and/or installation of additional fish passage facilities at 

the Howland and Lowell Tannery dams are to be undertaken. 

PRFP Page 70

17.2.4 Assess Fish Passage Improvements for Juvenile and Adult Alewife at 

Howland and Lowell Tannery 

A minimum of three field seasons are needed to verify that the improvements at 

Howland and Lowell Tannery allow the fish passage facilities to meet efficiency 

goals for passage of juvenile and adult alewife. 

17.3.1 Review the FERC License and Lower Penobscot River Multiparty 


Howland for Juvenile and Adult American Shad and Blueback Herring 

The hydro license for the Howland Project needs review to determine what articles, if 

any, were included by FERC that address fish passage. Similarly, the MPA contains 

specific language on fish passage provisions that could affect timelines listed in the 

work plan. Additionally, the MPA spells out specific fish passage strategies 

depending on whether the Veazie and Great Works dams are removed and the 

Howland Dam is bypassed as well as to which entity would be responsible for 

funding, installing, and operating the fish passage facilities. 



Juvenile and Adult American Shad and Blueback Herring 

The Howland fish passage facility, installed in 1965, has not been assessed for the 

passage of juvenile and adult American shad and blueback herring since it was 

primarily constructed for passage of Atlantic salmon. Studies of the existing 

upstream and downstream fish passage facilities and/or operational measures (e.g. 

cycling turbines, opening sluice gates, temporary shutdown of generation) need to 

be undertaken to ensure the existing passage facilities function properly and are 

effective in passing American shad and blueback herring. Any newly constructed 

fish passage facilities (e.g. Howland bypass) will need to undergo rigorous testing to 

ensure they function properly and are effective in passing American shad and 

blueback herring. All studies should be undertaken over the course of a minimum of 

three field seasons after Phase 1 habitat located above the Howland Dam is 

stocked. 


Studies 

Once fish passage efficiency studies are complete, redesign of existing facilities or 

bypass, operational changes to the existing facilities or bypass, and/or installation of 

additional fish passage facilities at the Howland Dam are to be undertaken. 

17.3.4 Assess Fish Passage Improvements for Juvenile and Adult American 

Shad and Blueback Herring at Howland 

A minimum of three field seasons are needed to verify that the improvements at 

Howland allow the fish passage facilities to meet efficiency goals for passage of 

juvenile and adult American shad and blueback herring. 

PRFP Page 71

17.4.1 Review FERC Licenses and FERC License Exemptions for Specific Fish 

Passage Deliverables for Juvenile and Adult Alewife, American Shad, and 

Blueback Herring at Remaining Tributary Dams 



that address fish passage. 



for Juvenile and Adult Alewife, American Shad, and Blueback Herring 



target restoration fish species. How fish passage improvements are addressed 

needs to be explored to develop options and approaches to ensure fish passage 

facilities meet established goals. 



Juvenile and Adult Alewife, American Shad, and Blueback Herring at 

Remaining Tributary Dams within 40 Years 

None of the existing upstream fish passage facilities on tributary dams have been 

assessed for the passage of juvenile and adult alewife, American shad, and 

blueback herring. Downstream fish passage facilities have been constructed at 

some but not all of the tributary dams and downstream passage operational 

measures (e.g. cycling turbines, opening sluice gates, temporary shutdown of 

generation) may be used to pass fish downstream of a hydro project. Studies of 

existing fish passage facilities will need to be undertaken to further understand 

bottlenecks and/or poor performance of existing fish passage facilities to make them 

more effective in successfully passing juvenile and adult alewife, American shad, 

and blueback herring around tributary hydro projects and non-hydro dams. Any 

newly constructed fish passage facilities will need to undergo rigorous testing to 



field seasons following stocking of habitat located upstream of the dams. 


Studies 



passage facilities at the remaining tributary dams are to be undertaken. 

17.4.5 Assess Fish Passage Improvements for Juvenile and Adult Alewife, 

American Shad, and Blueback Herring at Remaining Tributary Dams 

A minimum of three field seasons are needed to verify that the improvements at the 

remaining tributary dams allow the fish passage facilities to meet efficiency goals for 

passage of juvenile and adult alewife, American shad, and blueback herring. 

PRFP Page 72

17.5.1 Review the FERC License and Lower Penobscot River Multiparty 


Howland for Juvenile and Adult American Eel 

The hydro license issued for the Howland Project needs review to determine what 

articles, if any, were included by FERC that address fish passage. Similarly, the 

MPA contains specific language on fish passage provisions that could affect 

timelines listed in the work plan. Additionally, the MPA spells out specific fish 

passage strategies depending on whether the Veazie and Great Works dams are 

removed and the Howland Dam is bypassed as well as to which entity would be 

responsible for funding, installing, and operating the fish passage facilities. 




operators attempting to determine the efficiency of fish passage facilities for adult 

and juvenile American eel. There is a need to synthesize this information to provide 

for baseline conditions and to inform future studies and management decisions. 


Studies, and Develop Recommendations for Fish Passage Improvements at 

Howland within 10 years 

Once the review outlined in 17.5.2 is complete, studies of any newly constructed fish 

passage facilities and Howland bypass will need to undergo rigorous testing to 



field seasons within 10 years. 

17.5.4 Complete Fish Passage Improvements at Howland Based on Passage 

Efficiency Studies 

Once fish passage efficiency studies are complete, redesign of existing facilities or 

bypass, operational changes to existing facilities or bypass, and/or installation of 

additional fish passage facilities at the Howland Dam are to be undertaken. 

17.5.5 Assess Fish Passage Improvements for American Eel at Howland 


the fish passage facilities to meet efficiency goals for passage of juvenile and adult 

American eel. 

17.6.1 Review FERC Licenses and FERC License Exemptions for Specific Fish 

Passage Deliverables at Remaining Tributary Dams for Juvenile and Adult 

American Eel 



that address fish passage. 

PRFP Page 73



for Juvenile and Adult American Eel 



target restoration fish species. How fish passage improvements are addressed 

needs to be explored to develop options and approaches to ensure fish passage 

facilities meet established goals. 




operators attempting to determine the efficiency of fish passage facilities for adult 

and juvenile American eel. There is a need to synthesize this information to provide 

for baseline conditions and to inform future studies and management decisions. 

17.6.4 Utilize Annual Boat Electrofishing Surveys to Determine Requirement 

and Assessment Timeline for Fish Passage Facilities at Remaining Tributary 

Dams 

Boat electrofishing surveys will be undertaken annually to establish the need for fish 

passage facility installation and to determine the assessment timeline of existing 

passage facilities at tributary dams. 


Studies, and Develop Recommendations for Fish Passage Improvements at 

Remaining Tributary Dams within 30 years 

Once the review outlined in 17.6.3 and survey results outlined in 17.6.4 are 

complete, studies of existing fish passage facilities and for installation of new fish 

passage facilities at remaining dams will need to be undertaken. Any newly 

constructed fish passage facilities will need to undergo rigorous testing to ensure 

they function properly and are effective in passing the target restoration fish species. 

All studies should be undertaken over the course of a minimum of three field 

seasons within 30 years. 

17.6.6 Complete Fish Passage Improvements at Remaining Tributary Dams 

Based on Passage Efficiency Studies 


operational changes to existing facilities, and/or installation of additional fish 

passage facilities at the remaining tributary dams are to be undertaken. 

17.6.7 Assess Fish Passage Improvements at Remaining Tributary Dams 


the fish passage facilities to meet efficiency goals for passage of juvenile and adult 

American eel. 

PRFP Page 74


Passage Efficiency at FERC Non-Jurisdictional Dams at Lake and Pond 

Outlets 

Dams at outlets to larger lakes (e.g. Grand Lake Matagamon, Schoodic Lake) within 

the Penobscot drainage have been deemed non-jurisdictional by FERC because of 

limited benefits to downstream hydro generation. How fish passage improvements 

are addressed at these locations needs to be explored to develop options and 

approaches to ensure fish passage facilities or measures meet established goals. 


Studies, and Develop Recommendations for Upstream and Downstream Fish 

Passage for Juvenile and Adult Atlantic Salmon at the Grand Lake Matagamon 

Dam within 20 Years 

The existing upstream fish passage facility at Grand Lake Matagamon Dam was 

installed in 1942 with the primary target fish species being resident species. 

However, the existing fishway allows for passage of adult Atlantic salmon into the 

lake to access habitat in the upper East Branch, Penobscot River, including Webster 

Stream. Passage efficiency at this site has never been determined. There are no 

downstream passage facilities at the dam but gates are operated seasonally to 

regulate flows to the East Branch, Penobscot River. There is a need to understand 

the effectiveness of the upstream fish passage facility and if downstream passage is 

effective under the current water flow management regime to determine if upgrades 

are needed to make the fish passage facility and measures more effective in 

successfully passing juvenile and adult Atlantic salmon at the dam. All studies 

should be undertaken over the course of a minimum of three field seasons to ensure 

upstream and downstream passage effectiveness. 


Studies 


operational changes to existing facilities, and/or installation of additional fish 

passage facilities at the Grand Lake Matagamon Dam are to be undertaken. 


Salmon at the Grand Lake Matagamon Dam 


the fish passage facilities/measures to meet efficiency goals for passage of juvenile 

and adult Atlantic salmon. 


Passage Efficiency for Juvenile and Adult Alewife and American Eel at Lake 

and Pond Outlets 

Numerous lakes and ponds in the Penobscot River watershed have outlet dams, 

which may or may not have fish passage facilities. How fish passage improvements 

are addressed at these locations needs to be explored to develop options and 

approaches to ensure fish passage facilities or measures meet established goals. 

PRFP Page 75


Studies, and Develop Recommendations for Upstream and Downstream Fish 

Passage Improvements for Juvenile and Adult Alewife and American Eel at 

Lake and Pond Outlets within 50 Years 

Lake and pond outlet dams may inhibit passage of adult alewife and juvenile eel into 

lakes or ponds and low outflows at outlets during the emigration of juvenile and 

spent adult alewives and maturing eels may impede the timely downstream passage 

of alewives and eels. Studies are needed to understand what facilities or measures 

may be needed to meet fish passage efficiency goals and ensure passage of 

juvenile and adult alewife and American eel into and out of lakes and ponds. 


Studies 

Once fish passage efficiency studies are complete, installation of passage facilities, 

operational changes to existing passage facilities, and/or installation of additional 

fish passage facilities at lake and pond outlets are to be undertaken 

18.2.4. Assess Fish Passage Facility Improvements for Juvenile and Adult 

Alewife and American Eel at Lake and Pond Outlets 


the fish passage facilities/measures to meet efficiency goals for passage of adult 

and juvenile alewife and American eel. 

19.1.1 Review Need to Establish Upstream and Downstream Fish Passage 

Facility Operating Protocols to Ensure Proper Operation of Upstream and 

Downstream Fish Passage Facilities 

There is a need to monitor the operation of upstream and downstream fish passage 

facilities to ensure proper operation of the facilities during the migration season of 

the target restoration species. In some instances, particularly at hydro projects 

which have FERC license exemptions, operating protocols may not be included in 

articles within the FERC license or license exemption. There is a need to establish 

fish migration windows for the target restoration species so that all fish passage 

facilities are operated during the same time frames. 

19.1.2 Periodically Inspect Upstream and Downstream Fish Passage Facilities 

to Ensure Facilities are Effective in Passing Target Restoration Species 

Weekly inspections of fish passage facilities need to be undertaken to ensure proper 

and timely operation of the facilities. 

19.1.3 Consult with Owners of Fish Passage Facilities Regarding Fish Passage 

Issues 

Periodic maintenance at dams, ill-timed water releases, poor maintenance of fish 

passages facilities, etc. can result in poor fish passage. Consultation with dam 

owners prior to circumstances that cause less effective fish passage is necessary to 

prevent situations where access to spawning and rearing habitat is compromised. 

PRFP Page 76

19.1.4 Consult and/or Partner with Owners of Fish Passage Facilities to 

Improve Effectiveness of Fish Passage Facilities and/or Fish Passage 

Measures 

Fish passage facilities may be constructed as “state-of-the-art” yet may fall short of 

meeting fish passage efficiency goals. Similarly, measures may be instituted but 

could be ill-timed to benefit target restoration species. Consultation and/or forming 

partnerships with owners of fish passage facilities to improve the effectiveness of 

facilities and/or measures may be needed to meet fish passage targets. 

19.1.5 Consult and/or Partner with Dam Owners to Install Fish Passage 

Facilities at Problematic Passage Sites 

Dam owners may have constructed fish passage facilities that comply with fish 

passage articles within FERC license or license exemptions. However, some 

facilities may perform poorly. In other situations, fish passage facilities have yet to 

be installed. Depending on the dam (hydro, non-hydro), state or federal regulatory 

agencies may have authority to prescribe or request that fish passage facilities be 

installed and operated. USFWS and NOAA have prescriptive authority under 

Section 18 of the Federal Power Act to prescribe installation and operation of fish 

passage facilities at FERC jurisdictional dams. DMR and IFW have statutory 

authority to request installation of fish passage facilities at FERC non-jurisdictional 

dams. Consultation and/or forming partnerships with dam owners may be 

necessary to ensure passage of target restoration species at problematic sites. 

19.1.6 Develop Fish Handling and Trap Operating Protocols for the Milford 

Dam Fish Lift 

A new fish lift will be constructed at the Milford Dam in the next two or three years as 

part of the Penobscot River Restoration Project. MDDMR will be the primary agency 

involved with the operation of the lift. Atlantic salmon brood stock will be collected at 

this facility and clupeids will be sorted for release into the Milford headpond and/or 

transported to targeted river reaches or lakes and ponds. There is a need to 

develop protocols for fish handling, sorting, and operating the trap. 

20.1.1 Monitor Stream Connectivity to Ensure Effective Upstream and 

Downstream Fish Passage and Instream Movements 

Stream connectivity is crucial for target restoration species to access spawning and 

rearing habitat and to access the ocean. Stream connectivity is also critical for 

stream dwelling juvenile life stages to access food and refuge. Establishing a 

system for monitoring stream connectivity will ensure unimpeded access to various 

habitats within the Penobscot River watershed. 

20.1.2 Ensure Implementation of the Maine Department of Transportation’s 

Waterway and Wildlife Crossing Policy and Design Guide 

Numerous state and federal regulatory and resource agencies collaborated with 

MDOT in developing the policy and design guide. While the document guides 

development of effective ways to build, repair, and maintain the transportation 

PRFP Page 77

infrastructure, it does so by protecting important aquatic, wildlife, and surface water 

resources. The document was developed for planners, engineers, and designers 

working on MDOT projects. There are numerous municipalities, towns, and private 

landowners within the Penobscot River watershed that are unaware of the policy and 

design guide or have not adopted the guide in their planning, construction, and 

repair of road projects. There is a need for municipalities, towns, and private 

landowners to adopt the guide to direct their road construction and repair projects. 

Development of an education program, perhaps with the aid of MDOT, to get the 

municipalities, towns, and private landowners on board is needed. 

20.1.3 Identify Road Crossings and Small Barriers and Prioritize Passage 

Needs by Site and Fish Species 

An outcome of this task is to develop a prioritized list of specific road crossings and 

barriers that are crucial for passage of target restoration species. The list will serve 

to identify road crossings and barriers targeted for removal or replacement. 

20.1.4 Obtain Funding to Replace or Remove Problematic Road Crossing 

Structures and to Remove Critical Barriers 

Culverts, pipes, pipe arch bridges, or boxes of any type or size can impede 

movements of target restoration species if improperly sized and/or installed. A 

program to remove or upgrade road crossing structures to alleviate passage 

bottlenecks needs to be instituted. Similarly, small barriers can impede access to 

spawning and nursery habitats and/or refugia. Once problematic road crossings and 

small barriers have been identified and prioritized (Task 20.1.3), funding will be 

needed to remove critical barriers and/or replace road crossings that impede 

restoration of target species. 

20.1.5 Coordinate with Other State and Federal Agencies and NGOs to use a 

Standard Protocol and Tracking Database 

The State of Maine is convening a state coordinating meeting in April 2009 to initiate 

interagency coordination for restoring stream connectivity. The purpose of the 

meeting is to broadly define a goal for restoring stream connectivity and scope the 

feasibility of moving forward with a dedicated interagency effort. The vision is to 

have a coordinated prioritization, tracking and survey effort between state and 

federal agencies. 

20.1.6 Encourage Creation and Funding of a Barrier Removal Program in the 

State of Maine 

An extension of task 20.1.5 is to create and fund a barrier removal program that will 

address priority barriers in a coordinated way. 

20.1.7 Collaborate with Regulatory and Resource Agencies, Lake 

Associations, NGOs, etc. to Resolve Fish Passage Issues 

Fish passage at both dams and road crossings is a collaborative process, and some 

projects are more complex than others. In order to accomplish alewife restoration 

PRFP Page 78

goals, DMR will need to work with lake associations and other NGOs in order to 

obtain a permit from IFW. 

20.1.8 Research and Implement Alternative Methods for Habitat Access 

MDMR will work with MDIFW, USFWS, NOAA Barrier Owners, Land Owners and 

NGOs to seek innovative methods to improve connectivity to habitat. 

20.1.9 Undertake with Other Resource Agencies Risk Assessments of Range 

Expansion for Non-Native/Undesirable Fish Species 

Improving stream connectivity can lead to increased opportunities for range 

expansion of non-native/undesirable fish species whereas lack of stream 

connectivity can be detrimental to restoration of target species if specific life stages 

are unable to reach critical habitat at crucial times. This task is a placeholder within 

the Passage and Connectivity section. See Section 4 “Non-Native Species Including 

Northern Pike”, Tasks 23.1.2 and 23.1.3 for specific deliverables. 

20.2.1 Complete Ongoing Efforts to Catalogue Penobscot River Watershed 

Road Crossings and Small Barriers 

There have been several efforts over the past few years to survey and catalogue 

road-stream crossings and small barriers in the Penobscot River basin. The 

Kenduskeag Stream and the Piscataquis River watersheds have been surveyed by 

the USFWS and sections of the lower and mid-Penobscot River have been surveyed 

by a team led by the Maine Forest Service. Completion of this task will serve to 

identify where resources may be needed to correct stream connectivity problems. 

20.2.2 Determine Stream Connectivity Limitations for Juvenile and Adult 

Atlantic Salmon within 10 years 

Freedom of movement to and from the ocean as well as within the fresh water 

environment is necessary for Atlantic salmon to complete its life history. It is critical 

for smolts to reach the ocean and for adult Atlantic salmon to access spawning and 

rearing habitat and for kelts to migrate to the ocean and to return to spawning 

grounds as repeat spawners. It is also critical for juvenile salmon to have access to 

cool water during intervals of warm water temperatures and to shelter from frazil ice 

during winter. 

Once Task 20.2.1 is completed, connectivity limitations can be identified and 

prioritized. 

20.2.3 Undertake Stream Connectivity Improvements for Juvenile and Adult 


Once Tasks 20.1.3, 20.1.4, 20.2.1, and 20.2.2 are completed, resources can be 

allocated and stream connectivity problems for juvenile and adult Atlantic salmon 

remediated. 

20.3.1 Determine Stream Connectivity Limitations for Juvenile and Adult 

Alewife and American Eel within 50 years 

PRFP Page 79

Results of Tasks 20.1.3 and 20.2.2 should provide the bulk of necessary information 

to identify and prioritize stream connectivity limitations for alewife and American eel. 

20.3.2 Undertake Stream Connectivity Improvements for Juvenile and Adult 

Alewife and American Eel 

Once tasks 20.1.3, 20.1.4, 20.2.1, 20.2.2, and 20.3.1 are completed, resources can 

be allocated and stream connectivity problems for juvenile and adult alewife and 

American eel remediated. 

21.1.1 Develop a Memorandum of Understanding (MOU) with MDIFW for 

Selectively Removing Non-Native/Undesirable Fish Species at Fishway 

Passage Trapping Locations Prior to Removal of the Veazie and Great Works 

Dams 

An MOU between MDIFW and MDMR is needed to identify which non-native and 

undesirable fish species are to be removed from the Penobscot River at the Veazie 

and Mattaceunk fishway traps. If traps are installed at other fishways, then MOUs 

need to be developed for these trappings locations. 

21.1.2 Develop a Memorandum of Understanding (MOU) with MDIFW for 

Selectively Removing Non-Native/Undesirable Fish Species at the Milford Fish 

Lift Sorting Facility (Post Veazie and Great Works Dam Removals) 

An MOU between MDIFW and MDMR is needed to identify which non-native and 

undesirable fish species are to be removed from the Penobscot River at the Milford 

fish lift sorting facility after the Veazie and Great Works dams are removed. 

Specifics will be outlined in the Milford Fish Lift Operating Protocols developed in 

Task 19.1.6. 

21.1.3 Establish List of Non-Native/Undesirable Fish Species and Protocols for 

Removing or Allowing Passage at Fish Passage Facility Trapping Locations 

Non-native and undesirable fish species can be trapped at fishway traps as part of 

fish enumeration and brood stock collection operations. To prevent unintentional 

range expansion of non-native and undesirable fish species located downstream of 

fishway traps but not upstream, a list of fish species to be removed and protocols for 

removal will be established. For non-native and undesirable fish species already 

present upstream of trapping locations, protocols for removing or allowing passage 

will be established. 

21.1.4 Undertake with Other Resource Agencies Risk Assessments of Range 

Expansion for Non-Native/Undesirable Fish Species 

Installing and/or operating fish passage facilities without appropriate controls can 

increase range expansion of non-native/undesirable fish species. This task is a 

placeholder within the Passage and Connectivity section. See Section 4 “Non- 

Native Species Including Northern Pike”, Tasks 23.1.2 and 23.1.3 for specific 

deliverables. 

PRFP Page 80

21.1.5 Develop Memorandum of Understandings with Resource Agencies and 

Fish Passage Facility Operators to Prevent Upstream Movements of Non- 

Native/Undesirable Fish Species 

Once Tasks 21.1.3 and 21.1.4 are complete, agreements with resource agencies 

and fish passage facility operators will be instituted at fish passage facilities where 

traps are currently being operated. 

21.2.1 Assess with Other Resource Agencies the Need for Physical and/or 

Temporal Modifications to Fish Passage Facilities 

Structural modifications to existing fish passage facilities and/or temporal operation 

can lessen the opportunity for range expansion of non-native/undesirable fish 

species. However, modifications and/or temporal operation can impact movements 

of target restoration species. This task is a placeholder within the Passage and 

Connectivity section. See Section 4 “Non-Native Species Including Northern Pike”, 

Tasks 23.1.1.1, 23.1.1.3 and 23.1.1.3 for specific deliverables. 

21.2.2 Obtain Funding to Trap or Seasonally/Permanently Modify Fish Passage 

Facilities to Prevent Upstream Movement of Non-Native/Undesirable Fish 

Species 

Once risks assessments and the need for physical and/or temporal modifications to 

fish passage facilities are completed (Tasks 21.1.4 and 21.2.1), it may be necessary 

to seasonally modify or trap fish passage facilities to prevent upstream movements 

of non-native/undesirable fish species. At other fish passage facilities, it may be 

necessary to permanently modify them to prevent upstream movements of nonnative/undesirable 

fish species. Specific mechanisms to fund modifications or traps 

will be identified should modifications or trapping of fish passage facilities be 

deemed necessary. 

References 

Abbott, A. 2008. Maine Road-Stream Crossing Survey Manual. Gulf of Maine 

Coastal Program. U. S. Fish and Wildlife Service. Falmouth, Maine. 27 pp. 

FERC (Federal Energy Regulatory Commission). 2004. Handbook for hydroelectric 

project licensing and 5 MW exemptions from licensing. Federal Energy 

Regulatory Commission, Washington, D.C. 

Hotchkiss, R. H. and C. M. Frei. 2007. Design for Fish Passage at Roadway-Stream 

Crossings: Synthesis Report. Office of Infrastructure Research and 

Development. Turner-Fairbank Highway Research Center. Federal Highway 

Administration. McLean, VA. 

MDOT (Maine Department of Transportation). 2008. Waterway and wildlife crossing 

policy and design guide. Third edition. Maine Department of Transportation, 

Augusta, ME. 122 pp. 

PRFP Page 81

MFS (Maine Forest Service). 2008. 2007 Lower Penobscot River stream barrier 

surveys. In partnership with the U. S. Fish and Wildlife Service Gulf of Maine 

Coastal Program. Maine Forest Service, Augusta, ME 

MFS (Maine Forest Service). 2004. Best Management Practices for Forestry: 

Protecting Maine’s Water Quality. Maine Forest Service, Augusta, ME. 92 pp. 

NRC (National Research Council). 2004. Atlantic salmon in Maine. National 

Academy Press. Washington, D.C. 275 pp. 

Project SHARE. 2004. BMP Guidelines for Roads in Atlantic Salmon Watersheds. 

Restoration Working Group, Cherryfield, Maine, by Kleinschmidt Associates, 

Pittsfield, Maine. 

Stream-Simulation Group, USDA Forest Service. 2008. Stream Simulation: An 

Ecological Approach to Providing Passage for Aquatic Organisms at Road- 

Stream Crossings. U.S. Department of Agriculture, Forest Service, San Dimas 

Technology and Development Center. San Dimas, CA. 

USFWS (U.S. Fish and Wildlife Service). 2004a. Atlas of surveyed road crossings in 

the Kenduskeag Stream subdrainage. USFWS, East Orland, ME 

USFWS (U.S. Fish and Wildlife Service). 2004b. Surveyed road crossings and dams 

in the Piscataquis River drainage. USFWS, East Orland, ME 

PRFP Page 82

Section 3 - Habitat 

PRFP Page 83

Authors: Greg Mackey, Gail Wippelhauser and Melissa Laser 

Introduction 

Habitat is defined as an ecological or environmental area that is inhabited by a 

particular species; it is the natural environment in which an organism lives, or the 

physical environment that surrounds a species. For the purposes of this operational 

plan we consider characteristics of the water (e.g. quantity, velocity, temperature, 

dissolved and suspended inorganic or organic material) and the physical structure of 

the basin (e.g. width, depth, substrate type, substrate complexity, gradient) as 

important components of fish habitat to be protected or restored. 

The Strategic Plan identified man-made barriers that prevented access to spawning 

habitat as the major reason for the decline of diadromous fish populations in the 

Penobscot River. These barriers also have secondary impacts, because they alter 

the movement of water, sediment, and organic material through the watershed. 

Goals and objectives related to barriers are presented under Passage and 

Connectivity. 

The Strategic Plan identified impaired water quality on the mainstem as an important 

habitat issue, and species that spend most of their time in this area are at particular 

risk. For example, a large coal tar deposit is adjacent to a shortnose sturgeon 

overwintering area in Bangor, and mercury from the HoltraChem site in Orrington 

has bioaccumulated in tomcod. These pollutants may have less of an impact on life 

stages or species that spend less time in the lower river, for example, juvenile shad 

that feed on plankton for a few months or salmon smolts that emigrate in a few 

weeks. In contrast, water quality in tributaries where Atlantic salmon spawn may be 

more impacted by past and present forestry practices. Although water quality has 

been identified as an important issue, the Maine Department of Environmental 

Protection (MDEP) has statutory authority for maintaining or improving the quality of 

Maine’s surface waters. 

Background 

In time, a basin-wide watershed assessment will be conducted focusing on 

watershed processes (adapted from Roni et al. 2002). 

Watershed process Examples of assessment methods 

Sediment supply and erosion 

• Inventory sediment sources and calculate 

sediment budgets 

• Inventory roads for landslide hazard; list 

sites requiring restoration work 

PRFP Page 84

Hydrology 

Riparian and organic inputs 

Nutrients 

Light and heat inputs 

• Map surface erosion hazards (road 

surfaces and soils) 

• Inventory areas where boulders have been 

removed from streams 

• Assess changes in hydrologic regime due to 

increased impervious surface areas 

• Assess changes in peak flows resulting from 

rain-on-snow and extension of drainage 

networks by road ditches 

• Assess connectivity of wetlands, sloughs, and 

stream channels 

• Map riparian forest conditions to locate areas 

of low woody debris availability 

• Assess historical riparian vegetation including 

land use and fire history to understand 

changes in woody debris and organic matter 

inputs 

• Assess inorganic nutrient inputs based on 

geologic mapping 

• Assess current and historical diadromous fish 

escapement to examine changes in marinederived 

nutrients 

• Assess current and historical shading to 

estimate changes in stream temperature 

• Assess dams and other structures for changes 

in stream temperatures. 

The general approach is to review data from previously surveyed river reaches and 

use GIS technology to identify, map, and assess critical habitat for each species, to 

prioritize actions that will protect unimpaired habitat or restore impaired habitats, and 

to carry out these actions within 40 years. Habitat restoration and protection 

priorities are based on the Strategic Plan and Roni et al. (2002). Higher priority 

actions achieve the fastest response, are long-lasting, have a high probability of 

success, and impact the greatest number of species. 

Goals, Objectives and Strategies 

Goal: Restore and maintain a healthy aquatic ecosystem that conserves native 

biodiversity, manages or prevents the invasion of non-native aquatic species, 

increases the natural recruitment of fish, and improves aquatic habitat. 

PRFP Page 85

22.0 Objective: Protect or restore critical habitat for diadromous fish (spawning, 

nursery, feeding, overwintering) within 40 years. 

Measure: Complete 50% of necessary habitat identification, mapping, and 

assessment in all subwatersheds in five years, 75% in 15 years, and 100% in 25 

years. 

• Measure: Develop multi-species habitat protection and restoration plan in five 

years with a focus on key sub-drainages or river reaches targeted for earliest 


• Measure: Complete 10% of restoration projects in 10 years, 20% in 20 years, 

50% in 30 years, 70% in 40 years, and 100% in 50 years. 17 

• Measure: Improve current method of environmental review (hydropower review, 

DOT projects, MNPDES permits within 5 years. 

22.1 Strategy: Expand USFWS barrier model by adding existing layers 

(habitat historically and currently used by each species, water quality 

classifications, point source discharges, non-native species) within two 

years. 

22.2 Strategy: Develop GIS model(s) to predict the location and amount of 

Atlantic salmon habitat in the watershed within 3 years and verify model(s) 

with existing on-the- ground surveys. 

22.3 Strategy: Conduct expanded DMR “Big River” physical habitat surveys 

on stratified random sample of habitat types within five years to provide data 

to verify the salmon GIS model(s). 

22.4 Strategy: Maintain or expand water temperature measurements in 

salmon habitat over the next five years, but incorporate into a unified plan for 

the basin. 

22.5 Strategy: For 11 other species conduct studies (e.g. telemetry) or 

survey (e.g. visual or auditory) to identify spawning, nursery, feeding, and 

overwintering habitat as appropriate, and incorporate into USFWS barrier 

model within five years. 

22.6 Strategy: Prioritize restoration projects for each species per Roni et al. 

(2002): 

a. Protect unimpaired habitat. 

b. Reconnect isolated habitats. 

c. Improve/remove roads that alter hydrology, sediment, organic 

material. 

d. Increase nutrients to salmon waters if levels are low. 

e. Restore riparian processes (shade, sediment storage, water 

storage, bank stabilization, stream complexity). 

f. Restore instream habitat (woody debris, boulders). 

22.7 Strategy: Revisit the water management plan for the one major water 

control structure in the drainage Grand Lake Matagamon 

a. Determine how the existing plan affects habitat availability, 

geomorphic and hydrologic functions in the East Branch. 

17 See Passage and connectivity for schedule for barrier projects. 

PRFP Page 86

22.8 Strategy: Undertake an IFIM to pinpoint seasonally habitat protective flows 

22.9 Strategy: In priority areas, remove or repair roads that impair watershed 

processes. 

22.10 Strategy: In priority areas, increase productivity of salmon habitat by restoring 

diadromous fish (assuming habitat is suitable for other diadromous species). 

22.11 Strategy: In priority areas, restore riparian processes. 

22.12 Strategy: In priority areas, increase stream complexity in low large wood 

areas or known boulder removal areas. Increase stream complexity in 20 % of 1 

sub-basin’s streams 2-7 m in width in 10 years, 20 % of another sub-basin’s 

streams 2-7 m in width in 20 years, and 20 % of a third sub-basin’s streams 2-7 

m in width in 10 years. 

22.13 Strategy: Use the PITS model to help set restoration goals and to help identify 

and prioritize restoration opportunities 



Specialists and two seasonal Conservation Aides. Budget is estimated for 2010- 

2014. 


22.1 Expand USFWS barrier model to 

include other species and variables 

(to serve as model for prioritization) 

22.1.1 Assemble and assess water quality 

data to determine potential 

productivity of lacustrine and 

riverine habitat for diadromous 

fishes. 

22.2 Develop GIS models for predicting 

salmon habitat 

22.2.1 Use GIS model(s) to predict the 

location and amount of Atlantic 

salmon habitat. 

22.3 Conduct DMR BSRFH “Big 

River”Field survey 

22.3.1 Use "Big River" field data from to 

validate model output. 

22.3.2 Define sampling frame for Big 

River surveys based on stream 

types, size, gradient, geographic 

location. 

22.4 Maintain or expand temperature 

monitoring 

22.4 Use available temperature data to 

evaluate potential interactions of 

Atlantic salmon with non-native 

invasive species 

2009 USFWS $0 

2010 DMR/DEP $0 

2009 USFWS/NOAA $0 

2009 USFWS/NOAA $0 

2010-2012 DMR $120,000 

2010-2012 DMR $6,204 

2010-2012 DMR $6,204 

Annual DMR $25,000 

Annual DMR $0 

PRFP Page 87

22.4 Use additional information and 

data to indicate habitat quality 

(temperature, gradients, drainage 

area etc.). 

22.4 and 

22.5 

Review or acquire baseline water 

chemistry data in all critical 

habitats. 

22.5 Condcut studies for other species 

to identify habitat 

22.6 Develop method to assess key 

qualitative habitat features 

(embeddedness, substrate type, 

large wood, etc.) and 

systematically address these 

ideas. 

22.6 Establish team to develop 

watershed assessment plan 

2010 DMR $0 

2011 DMR $0 

2009-2014 DMR $250,000 

2009-2014 DMR $250,000 

2010 DMR and partners $0 

22.6 Develop habitat 

protection/restoration plan 

2011+ DMR and partners $25,000 

22.6 Conduct a basin-wide watershed 

assessment per Roni et al.( 2002). 

2009-2014 DMR $250,000 

22.6.1 Examine the factors limiting 

Atlantic salmon juvenile production 

at Katahdin Iron Works area on the 

Pleasant River. 

2010 DMR $0 

22.7 Revisit the water management plan 

for the one major water 

control structure in the drainage 

$0 

Grand Lake Matagamon 2010 DMR/DEP 

22.8 Undertake an IFIM to 

pinpoint seasonally habitat 

protective flows 

2010 DMR $0 

22.9 Remove or repair roads that impair Annaul 

watershed processes 

DMR/DOT/MFS $1,000,000 

22.10 Support studies of MDN inputs to 

the basin (see Issue 7) 

Annual DMR/NOAA $0 

22.11 Identify areas for riparian forest 

improvement and pursue 

improvements. 

22.11 and 

22.12 

Complete restoration/protection 

projects 

22.12 Increase complexity by adding 

large wood or boulders 

22.12.1 Predict LWD loadings in other 

streams using an LWD loading 

model based on forest stand data, 

environmental variables, and 

stochastic events. 

22.13 Use PITS model to set restoration 

goals 

Annual DMF/IFW/MFS $25,000 

Annual DMR/NGOs $2,500,000 

Annual DMR/IFW/MFS $500,000 

2010 DMR/USFS/MFS $45,000 

2010 NOAA $0 

PRFP Page 88


22.1 Expand USFWS barrier model by adding existing layers. 

22.2 Develop GIS model(s) to predict the location and amount of Atlantic 

salmon habitat in the watershed within 3 years. 

In smaller watersheds, salmon habitat typically has been mapped and identified by 

foot or boat survey or on-the-water surveys. This approach is not practical for the 

Penobscot watershed, which is the largest in Maine. The development of GIS 

model(s) to predict the location and amount of Atlantic salmon habitat will provide 

more information faster (with estimates of precision) at lower cost than surveys of 

the entire watershed. Model out puts will be verified with existing data. 

22.3 Conduct expanded DMR “Big River” physical habitat surveys to provide 

data to verify the salmon GIS model(s). 

Field surveys of habitat should continue to use the DMR BSRFH “Big River” habitat 

survey method and focus on waters of importance to salmon management, but also 

focus on surveying a diversity of stream types (size, gradient, geographic location). 

Expand the survey to include observation on large wood, connectivity, 

embeddedness, substrate type, etc. This will help managers understand the scope 

and frequency of habitat across various stream types. Such surveys will also help to 

validate modeling efforts, providing more and faster habitat information with 

estimates of precision at lower cost. A sampling plan for habitat survey will be 

established by biologists familiar with the basin and with the GIS habitat model. 

Such a survey may include stream reaches randomly chosen for a defined sampling 

frame. On an annual basis, a portion of each summer will be allotted to habitat 

survey, with balance between habitat assessment and survey. 

22.4 Maintain or expand water temperature measurements in salmon habitat. 

Water temperature monitoring in the Penobscot basin falls within a larger state-wide 

water temperature monitoring plan for Atlantic salmon waters. Recently, DMR 

BSRFH has been scaling back the number of temperature loggers deployed 

annually, and is concentrating on monitoring key index sites and using additional 

loggers to rotate among sites for interest. This correlates water temperatures at new 

sites to the index site(s) and allows a prediction model to be constructed. Water 

temperature should continue to be recorded at index sites, while additional loggers 

shall be deployed at sites of interest. New sites may be chosen using a GTRS 

method. This will provide unbiased water temperature information for the basin. 

The amount of effort to put into water temperature monitoring should be kept at or 

below current levels, unless a well-defined study is put forth. More effort should be 

put into analysis and interpretation of water temperature data. Notably, a stream 

classification system should be finalized and put into general use statewide. 

22.5 For other species conduct studies (e.g. telemetry, hydroacoustics) or 

survey (e.g. visual or auditory) to identify spawning, nursery, feeding, and 

overwintering habitat as appropriate. 

PRFP Page 89

Identifying and mapping important habitat for other diadromous species can be 

accomplished in a variety of ways. Acoustic telemetry is currently being used to 

locate habitat used by shortnose and Atlantic sturgeon. American shad and 

blueback herring typically spawn in a few distinct areas that can be located by visual 

or auditory surveys conducted in a few days. Sea lamprey redds also can be 

located visually. Hydroacoustic techniques may be appropriate for rainbow smelt. 

Alewife spawning and nursery habitat can be assumed to be an entire lake. 

22.6 Prioritize restoration projects for each species per Roni et al. (2002) 

Each species habitat will be examined and prioritized in order to: protect unimpaired 

habitat, reconnect isolated habitats, improve/remove roads that alter hydrology, 

sediment, organic material, increase nutrients to salmon waters if levels are low, 

restore riparian processes (shade, sediment storage, water storage, bank 

stabilization, stream complexity) and restore instream habitat (woody debris, 

boulders). The habitat objectives, measurables and tasks will require an in depth 

planning process to make them operational. Assemble small team with members 

with watershed knowledge and watershed assessment and restoration expertise. To 

conduct a watershed assessment, NGO watershed groups will be required in 

addition to government agencies. Formation of effective watershed NGO(s) is a 

prerequisite to a watershed assessment. 

22.7 Revisit the water management plan for the one major water 

control structure in the drainage Grand Lake Matagamon 

Determine how the existing plan affects habitat availability, geomorphic and 

hydrologic functions in the East Branch. 

22.8 Undertake an IFIM to pinpoint seasonally habitat protective flows 

22.9 In priority areas, remove or repair roads that impair watershed processes. 

Based on 22.1 and 22.6, problematic roads and road crossing will be addressed. 

22.10 In priority areas, increase productivity of salmon habitat by restoring 

diadromous fish (assuming habitat is suitable for other diadromous species). 

This strategy ties into Section 1 of the plan. 

22.11 In priority areas, restore riparian processes. 

Riparian processes are closely linked to habitat complexity and water quality and are 

an element of lateral and vertical connectivity. Based on the land use history and 

forest growth models, riparian forests will be restored. DMR will work closely with 

the Maine Forest Service on this strategy. 

22.12 In priority areas, increase stream complexity in low large wood areas or 

known boulder removal areas. Increase stream complexity in 20 % of 1 subbasin’s 

streams 2-7 m in width in 10 years, 20 % of another sub-basin’s 

streams 2-7 m in width in 20 years, and 20 % of a third sub-basin’s streams 2-7 

m in width in 10 years. 

PRFP Page 90

Recent surveys in coastal Maine rivers have revealed that large woody debris (LWD) 

is at extremely low levels. A study is underway to test the effectiveness of adding 

LWD to salmon habitat. However, no surveys have been done in the Penobscot 

basin, nor in more inland Maine rivers. The Penobscot basin contains a wider array 

of land use activities, forest types, and landscape features than does the coastal 

area where previous surveys were done. Therefore, performing LWD surveys 

across reaches with different stream sizes, forest stands, topography, and land use 

history would help link LWD loading to these variables. Assuming a link is revealed, 

we can use this information to predict LWSD loadings in other streams. One avenue 

that may aid in this is using an LWD loading model based on forest stand data, 

environmental variables, and stochastic events. Field surveys will help validate the 

model and allow broader inferences to be made. 

23.13 Use the PITS model to help set restoration goals and to help identify 

and prioritize restoration opportunities 

The Penobscot River Restoration Project (PRRP) is a multimillion dollar endeavor 

that aims to restore self-sustaining populations of native sea-run fish through the 

removal of two mainstem dams and improved fish passage at numerous other dams 

on the Penobscot River. While many diadromous species will benefit from the 

PRRP directly, other species such as endangered Atlantic salmon (Salmo salar), 

alewife (Alosa psuedoharengus), and American shad (Alosa sapidissima) may 

require additional habitat improvements (barrier removal, fishways, etc.) or stocking. 

Thus, additional active restoration measures may be required to realize the full 

potential of the PRRP. Due to the high profile and high cost of the project as well as 

numerous state, federal and non-governmental organizations involved, there is a 

need to prioritize restoration efforts in the basin to increase the probability for project 

success. To help facilitate this goal, we have created an ecologically-based GIS tool 

to help set restoration goals and to help identify and prioritize restoration 

opportunities (stocking options, barrier removal, and fishway improvements). Initial 

data inputs for the model include spawning habitat for a shortened list of focal 

species, a habitat weighting variable, and passage barriers (location and passage 

state). The outputs of the model are ecologically-based targets for focal species and 

prioritized lists of restoration projects based on their biological merits, rather than 

being selected as opportunities arise. These outputs will help ensure that 

restoration efforts and money are targeted appropriately and that achievable goals 

are set. 

References 

Abbott, A. 2008. Maine Road-Stream Crossing Survey Manual. Gulf of Maine 

Coastal Program. U. S. Fish and Wildlife Service. Falmouth, Maine. 27 pp. 

Hotchkiss, R. H. and C. M. Frei. 2007. Design for Fish Passage at Roadway-Stream 

Crossings: Synthesis Report. Office of Infrastructure Research and 

Development. Turner-Fairbank Highway Research Center. Federal Highway 

Administration. McLean, VA. 

PRFP Page 91

Roni, P., T. J. Beechie, R. E. Bilby, F. E. Leonetti, M. M. Pollock, and G. R. Pess. 

2002. A Review of Stream Restoration Techniques and a Hierarchical Strategy 

for Prioritizing Restoration in Pacific Northwest Watersheds. North American 

Journal of Fisheries Management 22:1–20. 

Stream-Simulation Group, USDA Forest Service. 2008. Stream Simulation: An 

Ecological Approach to Providing Passage for Aquatic Organisms at Road- 

Stream Crossings. U.S. Department of Agriculture, Forest Service, San Dimas 

Technology and Development Center. San Dimas, CA. 

PRFP Page 92

Section 4 - Non-Native species including Northern pike 

PRFP Page 93

Authors: Authors: Melissa Laser (editor), Fred Seavey (USFWS), Richard Dill (MDIFW), Merry Gallagher (MDIFW), Tim 

Obrey (MDIFW), Jeff Reardon (Penobscot Trust), Rory Saunders (NOAA), Tara Trinko (NOAA), Joan Trial (MDMR), 

Peter Ruksznis (MDMR) 

Introduction 

Lack of access to habitat has been a major contributor to the decline of many 

species in the basin. This presents an enormous challenge for the resource 

agencies and other conservation interests who are actively involved in fish 

restoration efforts, given that dams and other barriers such as culverts have greatly 

reduced the amount and accessibility of spawning and rearing habitat that once was 

available. These barriers also serve to restrict the natural dispersal of non-native 

fishes. 

The intentional introduction of smallmouth bass into the watershed in the late 1860s 

led to its expansion throughout the watershed such that virtually every accessible, 

suitable habitat reach, including dozens of tributary lakes and ponds, has now been 

colonized and it is managed by MDIFW as a sport fish. Brown trout, an exotic 

species native to Europe, is stocked by MDIFW for recreational fishing. Chain 

pickerel, managed by MDIFW as sport fish, were introduced into Maine waters in the 

1800s and have been spread legally and illegally throughout the basin. Landlocked 

salmon and white perch are native to the Penobscot basin, but their range has been 

artificially expanded. Numerous other non-native fish species have since been 

introduced (some intentional, some illegal, some accidental) over more recent 

decades, which has exacerbated the problems associated with changes in 

community assemblages and food web interactions. Since 1983, black crappie, 

green sunfish, largemouth bass, white catfish, central mudminnow and northern pike 

have been illegally introduced into the Penobscot basin. 

Goal, Objectives and Strategies 

Goal: Restore and maintain a healthy aquatic ecosystem that conserves native 

biodiversity and manages or prevents the invasion of non-native aquatic species 

Objective 23: Restrict upstream passage of non-native species where risks are the 

greatest. 

Measure: Identified areas of concern 

24.1. Strategy: Perform risk assessments for non-native species prior to 

changes at fishways. 

23.1.1 Task: Implement the management actions from the Piscataquis River 

Northern Pike Risk assessment (see Appendix J) 

23.1.1.1 Third party survey of potential connections and a development 

of solutions between West Branch and the Pleasant (Immediate 

need Appendix K) - $15,000 

23.1.1.1.1.1 Ebeemee and the West Branch - 2009 

PRFP Page 94

23.1.1.1.1.2 East Branch Pond, which flows north and south to 

Nollesemic Lake to Shad Pond to the West Branch 

Penobscot below two impassable dams – 2009 

23.1.1.2 Maintain current blockages for pike in Sebec upper and lower 

until phase 1 of alewife restoration is complete and group 1 

American shad restoration is complete - 2009 

-Develop an MOU to re-visit in 2014 

23.1.1.3 Investigate and maintain current blockages for pike in Schoodic 

lower until phase 1 of alewife restoration is complete and group 

1 American shad restoration is complete - 2009 

-Develop an MOU to revisit in 2014 

23.1.1.4 Create velocity or jump barriers for pike while allowing Atlantic 

salmon to pass in D-F upper and lower and Guilford lower until 

phase 1 of alewife restoration is complete and group 1 

American shad restoration is complete - 2009 

-Develop an MOU to revisit in 2014 

23.1.1.5 Continue removal efforts at Pushaw - MDIFW cost one time 

$30,000 plus annual salary 2009 

23.1.1.6 E-fish around the known spawning areas to look for nursery 

areas - 2009 

23.1.1.7 Review current fishing regulations and develop 

recommendations for changes - 2009 

23.1.1.8 Review current education efforts and develop recommendations 

for changes – 2009 

23.1.1.9 Conduct a study of Pushaw Stream and Mud pond to look for 

juvenile pike 

23.1.1.10 Conduct habitat surveys of the Penobscot mainstem from 

Milford to Howland to determine the spatial distribution, quantity 

and quality of habitat patches necessary for upstream pike 

dispersal. 

23.1.1.11 Maintain public education efforts highlighting the permanent 

repercussions and costs associated with illegal fish stocking 

events – 2009 

23.1.1.12 Task: Design and implement a stratified random survey for nonnatives 

in the drainage – 2011 

23.1.1.13 LIDAR for the Penobscot drainage to get gradient data – 2010 

23.1.1.14 If feasible, install barriers between the Pleasant River and the 

West Branch Penobscot River - 2010 

23.1.2 Task: Conduct a risk assessment for northern pike in the rest of the 

drainage – 2010 

23.1.3 Task: Identify the need for risk assessments for other non-native 

species of concern – 2010 

23.2 Strategy: Work with interagency technical committee, lake associations 

and other NGOs to resolve passage issues. 

PRFP Page 95

23.2.1 Task: Hold an annual meeting between MDIFW and MDMR about 

limiting stocking of non-natives throughout the drainage – annual 

Objective 24: Minimize the ecological impact of non-native fishes. 

Measures: Maintain or reduce areas where non-native fishes are present. 

No future stocking of non-native fishes. 

24.1. Strategy: Assess the species-specific distribution and potential ecological 

threats of non-native fish species within the Penobscot basin. 

24.1.1. Task: Classify species-specific threats based on scientific literature to 

prioritize risk. 

24.1.2. Task: Conduct assessments where the literature fails to provide 

information. 

24.1.3. Task: Document dispersal following smallmouth bass introductions 

24.1.4. Task: Document dispersal following the illegal introduction of white perch 

in Moosehead Lake, Spencer Bay 

24.1.5. Task: Work cooperatively with University of Maine on smallmouth bass 

removal projects 

24.1.6. Task: Design a study in a small reach to investigate the impacts of nonnative 

species removal on stocked Atlantic salmon fry survival 

Objective 25: Minimize the occurrence and negative effects of invasive plants, 

invertebrates, and pathogens. 

Measures: Maintain or reduce areas where non-native species are present. 

25.1. Strategy: Work with MDEP to reduce the spread of invasive species. 

25.1.1.Task: Conduct an annual meeting with MDEP to keep up to date with 

issues in the drainage – Annual 

25.2. Strategy: Maintain bio-security program for fisheries sampling equipment 

25.2.1.Task: Coordinate interagency disinfection/bio-security protocols - 2009 



Specialists and four seasonal Conservation Aides. Budget is estimated for 2010- 

2014. 


Third party survey of potential 

connections and a development of 

solutions between the West Branch 

23.1.1.1 Penobscot River and the Pleasant River 2009 DMR/IFW $15,000 

Maintain current blockages for pike in 

Sebec upper and lower until phase 1 of 

alewife restoration is complete and group 

23.1.1.2 1 American shad restoration is complete 2009-2014 DMR/IFW $0 

PRFP Page 96

Investigate and maintain current 

blockages for pike in Schoodic lower until 

phase 1 of alewife restoration is complete 

and group 1 American shad restoration is 

23.1.1.3 complete. 

Create velocity or jump barriers for pike 

while allowing Atlantic salmon to pass in 

D-F upper and lower and Guilford lower 

until phase 1 of alewife restoration is 

complete and group 1 American shad 

2009 -2014 DMR/IFW $50,000 

23.1.1.4 restoration is complete 2009 -2014 DMR/IFW $50,000 

23.1.1.5 Continue removal efforts at Pushaw Annual IFW $150,000 

E-fish around the known spawning areas 

23.1.1.6 to look for nursery areas. Annual IFW $25,000 

Review current fishing regulations and 

23.1.1.7 develop recommendations for changes. 2009-2010 DMR/IFW $0 

Review current education efforts and 

23.1.1.8 develop recommendations for changes. 

Maintain public education efforts 

highlighting the permanent repercussions 

and costs associated with illegal fish 

2009-2010 DMR/IFW $10,000 

23.1.1.9 stocking events. Annual DMR/IFW $75,000 

Conduct a study of Pushaw Stream and 

23.1.1.10 Mud pond to look for juvenile pike 

Conduct habitat surveys of the 

Penobscot mainstem from Milford to 

Howland to determine the spatial 

distribution, quantity and quality of 

habitat patches necessary for upstream 

2009-2011 DMR/IFW $30,000 

23.1.1.11 pike dispersal. 

Design and implement a stratified 

random survey for non-natives in the 

2009-2011 DMR/IFW $30,000 

23.1.1.12 drainage Annual DMR/IFW $25,000 

LIDAR survey for gradient to get better 

data on potential movement of pike and 

23.1.1.13 location of additional natural barriers. 2010 DMR/IFW $0 

Conduct a risk assessment for Northern 

23.1.3 pike in the rest of the drainage 2010 Pike Workgroup $0 

Identify the need for risk assessments for 

23.1.3 other non-native species of concern 2010 ITC $0 

Hold an annual meeting between IFW 

and DMR about limiting stocking of non- 

23.2.1 natives throughout the drainage Annual IFW/DMR $0 

Classify species-specific threats based 

24.1.1 on scientific literature to prioritize risk. 2011 Pike Workgroup $0 

Conduct assessments where the 

24.1.2 literature fails to provide information. 2011 ITC $0 

Document dispersal following smallmouth 

24.1.3 bass introductions by 2013 ITC $0 

PRFP Page 97

Document dispersal following the illegal 

introduction of white perch in Moosehead 

24.1.4 Lake, Spencer Bay by 2012 ITC $0 

Work cooperatively with U Maine on 

24.1.5 smallmouth bass removal projects 

Design a study in a small reach to 

investigate the impacts of non-native 

species removal on stocked Atlantic 

Ongoing DMR/IFW $50,000 

24.1.6 salmon fry survival 

Conduct an annual meeting with DEP to 

keep up to date with issues in the 

2010 DMR $10,000 

25.1.1 drainage Annual DMR/ITC Chair $2,000 

Coordinate and implement interagency 

25.2.1 disinfection/bio-security protocols Annual ITC $6,000 


23.1.1. Implement the management actions from the Piscataquis River 

Northern Pike Risk assessment (see Appendix J) 

The risk assessment documents the timeline of events relating to the documentation 

of pike and the PRRP, the ecological risk of pike on native species, patterns of 

natural dispersal and human introductions, and focus areas for action. It concludes 

with management actions to reduce the impact of pike above the Howland bypass. 

23.1.1.1 and 23.1.1.14 Third party survey of potential connections and a 

development of solutions between the West Branch Penobscot River and the 

Pleasant River (see Appendix K) 

Two connections between the Piscataquis and the West Branch Penobscot were 

identified as concerns: 1) East Branch Lake has a north and south outlet where the 

North flows into the West Branch Penobscot and 2) a large wetland complex 

separates Ebeemee Lake, Sanborn Pond and Upper Jo-Mary Lake. These need to 

be surveyed and if feasible, install barriers between the Pleasant River and the West 

Branch Penobscot River. 

23.1.1.2 Maintain current blockages for pike in Sebec upper and lower until 

phase 1 of alewife restoration is complete and group 1 American shad 

restoration is complete 

The Sebec and Milo projects are both FERC-regulated, but were issued exemptions 

from licensing back in the 1980's. At the time, no conditions for fish passage were 

provided by the agencies, and are not included in the FERC orders for the projects, 

as is the case with most other more-recently issued exemptions (or licenses). At this 

time it is suggested that these barriers remain in place until alewife and shad 

restoration begin actively in this sub-watershed. 

23.1.1.3 Investigate and maintain current blockages for pike in Schoodic lower 

until phase 1 of alewife restoration is complete and group 1 American shad 

restoration is complete 

PRFP Page 98

The dam at Schoodic Lake has a 6’ dam with three gates – but at high water it may 

be passable. The dam should be assessed for passage and potentially altered to 

limit passage until alewife and shad restoration begin actively in this sub-watershed. 

23.1.1.4 Create velocity or jump barriers for pike while allowing Atlantic 

salmon to pass in D-F upper and lower and Guilford lower until phase 1 of 

alewife restoration is complete and group 1 American shad restoration is 

complete 

Three main stem dams, Brown's Mill (Dover-Foxcroft Lower), Moosehead 

Manufacturing (Dover-Foxcroft Upper), and Guilford (Interface), exist. All three have 

vertical slot fishways. Only Brown’s Mill has both upstream and downstream 

passage, although all three have upstream passage. The two dams in Dover- 

Foxcroft are hydro-electric facilities. At this time it is suggested that these fishways 

be altered with a jump barrier that still passes Atlantic salmon until alewife and shad 

restoration begin actively in this sub-watershed. 

23.1.1.5 and 23.1.1.6 and 23.1.1.10 Continue efforts in Pushaw drainage. 

This effort is ongoing. Spring removal efforts have been conducted for three years 

(2006-08) with some success. Night gill netting in the Pushaw Stream to target 

spawning pike was attempted in 2008, but unsuccessful. One day of gill netting was 

attempted in summer of 2006 in the deep hole around Mag's ledge, with zero pike 

captured. Fall trap netting and boat electrofishing was conducted in 2005 and 2008 

in an attempt to capture pike for radio tagging --- unsuccessful. E-fish around the 

known spawning areas to look for nursery areas. Conduct a study of Pushaw Stream 

and Mud Pond to look for juvenile pike 

23.1.1.7 Review current fishing regulations and develop recommendations for 

changes. 

IFW continues to explore all management practices that may negatively impact the 

pike population at Pushaw. This includes no management of pike that would benefit 

or promote a sport fishery for pike in the watershed. This effort should expand to the 

drainage as a whole. 

23.1.1.8 and 23.1.1.9 Review current education efforts and develop 

recommendations for changes. 

In winter 2006, signs were placed around Pushaw Lake and Mud Pond at public 

access points. Signs were also placed at local bait and tackle shops. In 

spring/summer 2006 signs were placed at boat launches along the Penobscot and 

Stillwater River advising anglers to be on the lookout for pike. These signs have 

produced some reportings, but follow up has resulted in no confirmation. In 2009 

signs will once again be placed (or replaced) Pushaw Lake, Mud Pond, Little 

Pushaw Lake, Pushaw Stream and at boat launches along the Penobscot and 

Stillwater River asking anglers to keep all pike if they catch them and to notify MIFW. 

Biological staff from both agencies have given presentations about the Pushaw Lake 

pike removal efforts, risks of illegal introductions, and the risk of pike to the upper 

Penobscot watershed to numerous local NGO's / grass roots organizations. Maintain 

PRFP Page 99

public education efforts highlighting the permanent repercussions and costs 

associated with illegal fish stocking events. 

23.1.1.11 Conduct habitat surveys of the Penobscot mainstem from Milford to 

Howland to determine the spatial distribution, quantity and quality of habitat 

patches necessary for upstream pike dispersal. 

23.1.1.12 Design and implement a stratified random survey for non-natives in 

the drainage 

Sampling natural systems for management requires unbiased and spatially 

distributed sampling, with samples spaced relatively evenly in space. Sampling 

must balance trend and status data collection goals. In addition, sampling should 

allow for greater emphasis (sampling) effort within certain areas depending on needs 

of biologists and managers. Finally, sampling must be flexible to allow un-sampled 

sites to be accounted for, and to add sites as needed. This requires a probability 

sampling approach. Without probability sampling we cannot understand how 

samples represent the “real world’ and are likely to collect biased data that may 

result in incorrect conclusions and inform poor management decisions. Clearly, this 

is vital for effective adaptive management. Furthermore, collecting data under a 

unified probability sampling plan with standardized protocols will greatly increase 

statistical power for the same level of sampling effort, allowing biologists to more 

powerfully analyze large spatial and temporal trends and status. Finally, the 

sampling plan for the Penobscot should be integrated with a larger state-wide 

sampling plan to increase statistical power and optimize the value of limited 

sampling capacity. 

23.1.1.13 LIDAR survey for gradient to get better data on potential movement 

of pike and location of additional natural barriers. 

23.1.2 Conduct a risk assessment for Northern pike in the rest of the drainage 

Replicate the process that was undertaken on the Piscataquis drainage, particularly 

in the area above West Enfield. 

23.1.3 and 24.1.1 and 24.1.2 Identify the need for risk assessments for other 

non-native species of concern 

Since 1983, black crappie, green sunfish, largemouth bass, central mudminnow, 

white catfish and northern pike have been illegally introduced into the Penobscot 

basin. Classify species-specific threats based on scientific literature to prioritize risk 

and conduct assessments where the literature fails to provide information. 

23.2.1 Hold an annual meeting between IFW and DMR about limiting stocking 

of non-natives throughout the drainage 

24.1.3 and 24.1.4 Document dispersal following smallmouth bass 

introductions and following the illegal introduction of white perch in 

Moosehead Lake, Spencer Bay 

PRFP Page 100

Work with IFW regional biologists to document small mouth bass and white perch to 

better understand human and natural dispersal. 

24.1.5 and 24.1.6 Smallmouth bass removal projects 

DMR will work cooperatively with U Maine on removal projects and will design a 

study in a small reach to investigate the impacts of non-native species removal on 

stocked Atlantic salmon fry survival. 

25.1.1 Conduct an annual meeting with DEP to keep up to date with issues in 

the drainage 

Either meet with DEP separately or actively participate in the Invasive Species Task 

Force. 

25.2.1 Coordinate and implement interagency disinfection/bio-security 

protocols 

PRFP Page 101

Section 5 - Analyze, Synthesize, and Communicate Results to Inform Future 

Adaptive Management Actions, Analyses, and Research 

PRFP Page 102

Authors: Joan Trial and Melissa Laser 

Introduction 

The plan’s overarching goal for the river is to restore and guide the management of 

diadromous fish populations, aquatic resources and the ecosystems on which they 

depend, for their intrinsic, ecological, economic, recreational, scientific, and 

educational values for use by the public. MDMR and MDIFW are the State agencies 

responsible for developing and carrying out the plan and the Maine Atlantic Salmon 

Commission has policy authority for Atlantic salmon. In addition, the Departments 

are working with the PIN, USFWS, NOAA Fisheries, who have federal trust 

responsibly for species included in the plan. The Departments are also working with 

the PRRT, PPL, researchers, other state and federal agencies and other 

stakeholders with an interest in the basin. The plan recognizes that restoring 

ecosystem processes and integrated multi-species fish management will increase 

potential success, and that working cooperatively with other State and Federal 

agencies, researchers and stakeholders are essential to the success of this effort. 

Fisheries management on the Penobscot River must also be integrated with regional 

and international management of diadromous species. 

The state plan presents a long-term vision and is intended to provide guidance to an 

interagency technical committee on restoration actions for multiple species over the 

next 25 years through the identification of shared goals, objectives and strategies for 

restoration, recovery, and management of multiple fish species and ecosystem 

processes, using an adaptive management approach. The key ecosystem 

processes are hydrology, connectivity, species assemblages, food web interactions, 

energy flow, and mineral cycles. Understanding these processes are going to 

require collaborative efforts with researchers and other state and federal agencies. 

Goal, Objectives and Strategies 

Goal: Coordinate fisheries management and restoration activities among state and 

federal fisheries agencies, PIN, and stakeholders and synthesize information. 

Objective 26: Cooperative management of the watershed that integrates ecosystem 

function and single species management. 

MEASURES 

o Number of Interagency meetings held annually 

o Frequency of updates to an Inventory of adaptive management systems 

o Frequency of updates to an Inventory of common standardized data collection 

methods 

o Frequency of updates to criterion list to guide cooperative management 

26.1. Task: Convene two interagency technical committee meetings annually to 

coordinate diadromous fish species research- annual 

PRFP Page 103

26.2. Task: Assemble adaptive management systems for active management of 

single species – by 2010 

26.3. Task: Identify shared information among adaptive management plans – by 

2010 

26.4. Task: Coordinate data collection and sharing among agencies - annual 

a. Standardize methods -by 2011 

26.5. Task: Identify potential interactions among species being managed - by 2012 

26.6. Task: Develop criteria that guide cooperative management where significant 

management conflicts are anticipated or identified – by 2012 

26.7. Task: Develop plans to discontinue stocking for all species with transfers or 

hatchery supplementation – by 2015 

Objective 27: Formalize a procedure to inform and consult stakeholders regarding 

existing or proposed management activities. 

MEASURES 

o Number of meetings with Lake Associations, angler groups, towns 

o Number and frequency of consultation meetings with FPL 

o Date of annual stakeholder meeting, number of attendees, agenda, 

discussion notes 

o Number and level of engagement for stakeholder groups 

o Number of communications among groups exchanging information related to 

management actions in the plan 

27.1 Task: Develop an outreach strategy that incorporates the tasks that follow 

and identifies additional ways to educate the general public on the benefits and 

importance of alewife restoration. 

27.2 Task: Hold interagency meetings with Phase 1 lake associations, angler 

groups, or towns – 2009 

27.3 Task: Develop consistent message about restoration plans with Trust, PIN, 

Services and State - 2009 

27.4 Task: Develop a mechanism to unify fisheries management information for 

stakeholders – by 2010 

27.5 Task: Consult annually with PPL and other dam owners on passage issues at 

their facilities – annual 

27.6 Task: Hold an interagency technical committee public meeting each year to 

present: – annual 

• program results and progress, 

• discuss potential management responses, 

• review proposed activities for the ensuing year 

27.7 Task: Develop new and enhance existing partnerships with stakeholders, 

which maximize resources available for achieving program objectives – annual 

27.8 Task: Continue to encourage communication and information exchange with 

those agencies, regulatory bodies, and organizations having related 

jurisdictional interests and responsibilities – annual 

PRFP Page 104

Objective 28: Support regional and international efforts relating to diadromous fish 

management and research. 

MEASURES 

o Number of regional management and assessment meetings attended by 

administrators and scientists 

o Number of international management and assessment meetings attended by 

administrative and scientists 

o Participation in setting regional and international research priorities 

o Funds or collaborative support expended for ongoing research at regional and 

international levels 

o Participation in meetings and products of Atlantic salmon Action Teams 

o Support and participation in UMaine and other universities/colleges research 

o Support and collaborative participant letters sent with research proposals 

28.1 Task: Participate in regional fisheries management and assessment efforts at 

both administrative and scientific levels – annual 

a. Atlantic Coastal Fish Habitat Partnership, 

b. New England Joint Venture, 

c. Atlantic States Marine Fisheries Commission, 

d. US Atlantic Salmon Assessment Committee, 

e. Eastern Brook Trout Joint Venture, 

f. New England Fish Administrators, 

g. New England Atlantic Salmon Coalition, 

28.2 Task: Participate in international management and assessment efforts such 

as the North Atlantic Salmon Conservation Organization and the International 

Council for the Exploration of the Seas – annual 

28.3 Task: Develop research priorities at regional and international levels – based 

on cycle of various organizations 

28.4 Task: Support ongoing research at regional and international levels – annual 

28.5 Task: Work closely with the Atlantic salmon Action Teams – annual 

Objective 29: Develop a better understanding of the human dimension of fisheries 

management through collaborating with partners. 

MEASURES 


(economics, human dimensions, land use) 


(economics, human dimensions, land use) 

o Number of changes in regulatory and management policies facilitated 

o Collaborative relationships with groups documenting land use in the 

watershed 

o Number of communications among groups exchanging information related to 

management actions in the plan (economics, human dimensions, land use) 

29.1 Task: Work with academic institutions to study the economic impacts of 

restoration of diadromous fish – annual 

PRFP Page 105

29.2 Task: Examine appropriate case studies and fisheries research, particularly 

with emphasis on the human dimension that can provide guidance for 

ecosystem-based management – annual 

29.3 Task: Work to understand community interest in the river – annual 

29.4 Task: Monitor and evaluate socio-cultural and economic interactions that 

contribute to and that occur as a result of ecosystem based fisheries 

management – annual 

29.5 Task: Improve communication among government groups – annual 

29.6 Task: Improve regulatory and management policies – annual 

29.7 Task: Develop a strategy to document land use changes in the Penobscot 

River – by 2012 

Objective 30: Work with University and other researchers to develop a better 

understanding of ecosystem processes in the Penobscot and their importance in the 

restoration of diadromous fishes (hydrology, connectivity, species assemblages, 

food web interactions, energy flow, and mineral cycles). 

MEASURES 

o Participation in Diadromous Species Restoration Research Network meetings 

(planning, science) 


(ecosystem processes, climate change) 


(ecosystem processes, climate change) 

30.1 Task: Participate in the Diadromous Species Restoration Research Network – 

Life of Project 

30.2 Task: Examine levels of marine derived and terrestrially derived nutrients, and 

macroinvertabrate and fish communities – annual 

30.3 Task: Examine role of climate change in altering ecosystem function and 

diadromous fish species population dynamics – annual 

30.4 Task: Participate in the Penobscot River Science Steering Committee 

30.5 Task: Examine the role of connectivity among main stems and tributaries and 

habitat types (rapids, flat waters, runs, riffles, pools), on productivity – annual 


The budget includes funding for three full-time Biologists and two full time Biology 

Specialists. Budget is estimated for 2010-2014. 


Convene two interagency technical 

committee (ITC) meetings annually to 

26.1 manage diadromous fish species 

Annual DMR / ITC Chair 

Assemble adaptive management 

systems for active management of single 

26.2 species 

by 2010 ITC 

Identify shared information among 

26.3 adaptive management plans. 

by 2010 ITC 

$87,000 

PRFP Page 106 

$0 

$0

Coordinate data collection and sharing 

26.4 among agencies 

Identify potential interactions among 

26.5 species being managed 

Develop criteria that guide cooperative 

management where significant 

management conflicts are anticipated or 

26.6 identified 

Develop plans to discontinue stocking 

for all species with transfers or hatchery 

26.7 supplementation 

Hold interagency meetings with Phase 1 

lake associations, angler groups, or 

27.1 towns 

Develop consistent message about 

restoration with Trust, PIN, Services and 

27.2 State 

Develop a mechanism to unify fisheries 

management information for 

27.3 stakeholders 

Consult annually with PPL and other dam 

owners on passage issues at their 

27.4 facilities. 

Hold an interagency technical committee 

27.5 public meeting each year. 

Develop new and enhance existing 

partnerships with stakeholders, which 

maximize resources available for 

27.6 achieving program objectives. 

Continue to encourage communication 

and information exchange with those 

agencies, regulatory bodies, and 

organizations having related jurisdictional 

interests and responsibilities. 

27.7 

Participate in regional fisheries 

management and assessment efforts at 

28.1 both administrative and scientific levels. 

a. Atlantic Coastal Fish Habitat 

28.1 Partnership, 

Annual ITC 

by 2012 ITC 

by 2012 ITC 

by 2015 DMR Bio III's 

2009 DMR / ITC Chair 

by 2010 DMR / ITC Chair 

by 2010 DMR / ITC Chair 



Annual ITC 

Annual ITC 

Annual DMR, IF&W 

Annual DMR 

$87,000 

$104,400 

$104,700 

$218,000 

PRFP Page 107 

$0 

$35,000 

$52,400 

$87,500 

$44,000 

$87,500 

$44,000 

0 

$44,000 

28.1 b. New England Joint Venture, Annual IF&W $44,000 

c. Atlantic States Marine Fisheries Annual DMR 

28.1 Commission, 

$44,000 

d. US Atlantic Salmon Assessment Annual DMR 

28.1 Committee, 

$89,500 

28.1 e. Eastern Brook Trout Joint Venture, Annual IF&W $44,000 

28.1 f. New England Fish Administrators, Annual DMR IF&W $44,000 

g. New England Atlantic Salmon Annual DMR 

28.1 Coalition, 

$44,000

Participate in international management 

and assessment efforts such as the 

North Atlantic Salmon Conservation 

Organization and the International 

Council for the Exploration of the Seas. 

28.2 

Develop research priorities at regional 

and international levels. 

Annual DMR 

based 

organization 

DMR IF&W 

$73,500 

28.3 

$0 

Support ongoing research at regional Annual DMR IF&W 

28.4 and international levels. 

$44,000 

Work closely with the Atlantic salmon Annual DMR IF&W 

28.5 Action Teams. 

$131,000 

Work with academic institutions to study 

the economic impacts of restoration of 

Annual DMR SPO 

29.1 diadromous fish. 

$44,000 

Examine appropriate case studies and 

fisheries research, particularly with 

emphasis on the human dimension that 

can provide guidance for ecosystem- 


29.2 based management. 

$44,000 

Work to understand community interest Annual DMR SPO 

29.3 in the river. 

$44,000 

Monitor and evaluate socio-cultural and 

economic interactions that contribute to 

and that occur as a result of ecosystem 


29.4 

based fisheries management. 

$44,000 

Improve communication among Annual DMR 

29.5 government groups. 

$44,000 

Improve regulatory and management Annual DMR 

29.6 policies. 

$44,000 

Develop a strategy to document land use by 2012 DMR SPO OGIS 

29.7 changes in the Penobscot River. 

$52,500 

Participate in the Diadromous Species 2008-2013 DMR 

30.1 Restoration Research Network 

$87,500 

Examine levels of marine derived and 

terrestrially derived nutrients, and 

Annual DMR USGS 

30.2 macroinvertabrate and fish communities. 

$44,000 

Examine role of climate change in 

altering ecosystem function and 

diadromous fish species population 

Annual DMR USGS 

30.3 dynamics. 

$44,000 

Participate in the Penobscot River Life of Group DMR 

30.4 Science Steering Committee 

Examine the role of connectivity among 

main stems and tributaries and habitat 

types (rapids, flat waters, runs, riffles, 

$87,500 

30.5 pools), on productivity Annual DMR MFS DOT $87,500 

PRFP Page 108


26.1. Convene two interagency technical committee meetings annually to 

manage diadromous fish species 

The State fisheries agencies, the Department of Marine Resources (MMDMR) and 

the Department of Inland Fisheries and Wildlife (MDIFW) are committed to working 

together and in cooperation with the Penobscot Indian Nation (PIN), the US Fish and 

Wildlife Service (USFWS), and National Oceanic and Atmospheric Administration 

National Marine Fisheries Service (NOAA Fisheries), and various NGOs in this 

effort. A primary responsibility of the interagency committee will be to address interagency 

management issues in areas of overlapping jurisdiction. 

26.2. Assemble adaptive management systems for active management of 

single species. 

As agencies and groups develop adaptive management systems for species or 

species groups, these will be compiled by the Interagency Technical Committee. 

26.3. Identify shared information among adaptive management plans 

As plans are compiled, the data needed to manage the individual species and 

species groups will be listed, and common information required for management can 

be identified. For example, stream electrofishing survey, habitat survey, riverine 

temperature and water quality data are likely to be required for Atlantic salmon and 

freshwater species management. 

26.4. Coordinate data collection and sharing among agencies, Standardize 

methods. 

An integrated sampling plan and common data structure for shared data will result in 

increased sampling and efficient data collection. Where similar habitat and 

population assessment techniques are used in adaptive management of several 

species or species groups, standard methods will increase sample coverage for all 

agencies. 

26.5. Identify potential interactions among species being managed 

At least 86 species of fish inhabit the Penobscot River basin (Baum 1983). Thirtyfive 

are found in marine or estuarine waters, 33 occur in freshwater, five species 

tolerate a range of salinities, and 12 are diadromous species that migrate between 

marine and freshwater habitats. All of the fishes are native to Maine with the 

exception of eight freshwater species. Since 1983, black crappie, green sunfish, 

largemouth bass, and northern pike have been illegally introduced into the 

Penobscot basin. Brown trout, an exotic species native to Europe, is stocked by 

MDIFW for recreational fishing. Chain pickerel and smallmouth bass, managed by 

MDIFW as sportfish, were introduced into Maine waters in the 1800s and have been 

spread legally and illegally throughout the basin. Landlocked salmon and white 

perch are native to the Penobscot basin, but their range has been artificially 

PRFP Page 109

expanded. This management plan focuses on the restoration of native diadromous 

fishes, which are all currently at less than 1% of historic levels. 

26.6. Develop criteria that guide cooperative management where significant 

management conflicts are anticipated or identified 

Develop a mechanism to coordinate management activities among state fisheries 

agencies and stakeholders in order to identify and resolve conflicts over fisheries 

restoration and management and develop criteria to resolve management conflicts 

that strike an appropriate balance in fish community structure compatible with 

individual agency objectives. 

26.7. Develop plans to discontinue stocking for all species with transfers or 

hatchery supplementation 

The ultimate goal is to have self-sustaining populations and therefore a plan will be 

developed to lessen and stop transfers or hatchery supplementation of all species 

over time. 

27.1. Hold interagency meetings with Phase 1 lake associations, angler 

groups, or towns 

In order to accomplish alewife restoration goals, MDMR will need to work with lake 

associations and other NGOs in order to obtain a permit from IFW. 

27.2 Develop consistent message about restoration plans with Trust, PIN, 

Services and State 

The role of stakeholders in the communities is to inform state representatives and 

administrative officials of fish restoration benefits and issues, to educate the public 

about the need to restore habitat, the challenges associated with restoring fisheries 

and the broad scope of fish restoration activities and to encourage citizens to inform 

their Local, State and Federal representatives of their support for fisheries 

restoration. It is therefore imperative that the major interested parties have the 

same message about the efforts in the Penobscot drainage. 

27.3 Develop a mechanism to unify fisheries management information for 

stakeholders 

Fisheries management information is spread throughout agency and regional 

reports. A compilation of these reports and summaries will provide easier public 

access to management decisions and the data supporting them for the Penobscot 

River. 

27.4 Consult annually with PPL and other dam owners on passage issues at 

their facilities 

MDMR will meet with PPL and other dam owners to keep an open dialogue going on 

passage issues in the drainage. 

PRFP Page 110

27.5 Hold an interagency technical committee public meeting each year to 

present: program results and progress, discuss potential management 

responses, review proposed activities for the ensuing year 

In order to inform stakeholders of the progress towards goals for the watershed and 

to update interested parties on the activities of MDMR, IFW and others working in 

the watershed, the ITC will host an annual meeting to keep a dialogue going with 

stakeholders. This is envisioned to have both a technical presentation component 

and a feedback session. 

27.6. Develop new and enhance existing partnerships with stakeholders, 

which maximize resources available for achieving program objectives 

There are multiple stakeholders in the drainage. Many are traditional watershed 

groups that are currently involved to some extent in restoration. MDMR will work to 

enhance these partnerships when possible. There are other non-traditional groups 

that MDMR will work towards including the process in order to achieve the desired 

results. 

27.7. Continue to encourage communication and information exchange with 

those agencies, regulatory bodies, and organizations having related 

jurisdictional interests and responsibilities 

Closely tied to tasks 29.5 and 29.6 to improve communication among government 

groups and improve regulatory and management policies. 

28.1. Participate in regional fisheries management and assessment efforts at 

both administrative and scientific levels 

The State of Maine participates in several inter-jurisdictional efforts including the 

Atlantic Coastal Fish Habitat Partnership, the New England Joint Venture, the 

Atlantic States Marine Fisheries Commission, the US Atlantic Salmon Assessment 

Committee, the Eastern Brook Trout Joint Venture, the New England Fish 

Administrators, and the New England Atlantic Salmon Coalition. 

28.2. Participate in international management and assessment efforts such as 

the North Atlantic Salmon Conservation Organization and the International 

Council for the Exploration of the Seas. 

The U.S. became a charter member of the NASCO in 1984. NASCO is charged with 

the international management of Atlantic salmon stocks on the high seas. Three 

Commissioners for the U.S. are appointed by the President and work under the 

auspices of the U.S. State Department. One of the Commissioners is from Maine. 

The International Council for the Exploration of the Seas (ICES), the official research 

arm of NASCO, convenes a Working Group on North Atlantic Salmon which is 

responsible for providing scientific advice to be used by NASCO members as a 

basis for formulating biologically sound management recommendations for the 

conservation of North Atlantic salmon stocks. The Working Group on North Atlantic 

Salmon, which is composed of representatives of member countries, including one 

Maine biologist and as many as three from the US, is responsible for the collecting 

and analyzing scientific data on salmon. 

PRFP Page 111

28.3. Develop research priorities at regional and international levels 

Same as 28.1 and 28.2 

28.4. Support ongoing research at regional and international levels 

Same as 28.1 and 28.2 

28.5. Work closely with the Atlantic salmon Action Teams 

Action Teams are the key component of the new Atlantic Salmon Recovery 

Framework. Activities (research and management actions) are identified and 

evaluated at the Action Team level. Each Action Team is charged with identifying 

the highest priority research and management actions that could be undertaken to 

further the recovery of the Gulf of Maine Distinct Population Segment of Atlantic 

salmon. Existing and new activities should be included in the list of activities and 

both compared against the same set of criteria. Each Action Team will use the 

same set of criteria to evaluate the conservation benefit of proposed activities. This 

will facilitate comparisons within Action Teams as well as across Action Teams. 

29.1. Work with academic institutions to study the economic impacts of 

restoration of diadromous fish 

For thousands of years, diadromous fishes migrated through much of the basin, 

providing a connection between the Gulf of Maine and inland terrestrial and aquatic 

ecosystems. For thousands of years, Native American’s living along the river and its 

tributaries have sought the migratory fish of the Penobscot River, as did the 

European explorers and settlers. Commercial harvest of the Penobscot River's 

migratory fish species began soon after the settlement of Bangor and Bucksport in 

the1760s. There is a need to understand what a restored population would mean to 

the economy of the region. 

29.2. Examine appropriate case studies and fisheries research, particularly 

with emphasis on the human dimension that can provide guidance for 

ecosystem-based management 

Restoring ecosystem processes and integrated multi-species fish management will 

increase potential success, and that working cooperatively with other State and 

Federal agencies, researchers and stakeholders are essential to the success of this 

effort. 

29.3. Work to understand community interest in the river 

There are many stakeholders with an interest in the watershed that have led and 

continue to lead restoration efforts. Various non-governmental organizations 

(NGOs) have worked to restore alewives by succeeding with three barriers removals 

in Souadabscook Stream, the removal of the Brownville Dam and active efforts to 

improve fish passage in Blackman Stream and Sedgeunkedunk Stream. 

Researchers from the University of Maine (UM) and other institutions have worked 

cooperatively with state and federal agencies, providing needed information on 

multiple fish species and the environment throughout the basin. The Penobscot 

PRFP Page 112

River Restoration Trust (PRRT or Trust) has worked tirelessly on the Penobscot 

River Restoration Project (PRRP). 

29.4. Monitor and evaluate socio-cultural and economic interactions that 

contribute to and that occur as a result of ecosystem based fisheries 

management 

The socio-economic processes of restoration have not traditionally been researched 

or addressed fully although a recent effort was attempted to assess these processes 

in regard to Atlantic salmon. A top priority is to attempt to re-engage the public in 

the recovery efforts in the basin, because apathy is a threat to recovery. The 

awareness, cooperation and participation of stakeholders, landowners, NGOs, public 

agencies, municipalities, and the general public are essential for restoration. 

Programs targeted at re-connecting people to the fish through a better 

understanding of the life history, habitat needs, economics, and importance to the 

people of Maine as well as the goals and objectives of recovery are crucial. 

29.5 and 29.6 Improve communication among government groups and 

improve regulatory and management policies 

The Interagency Technical Committee (task 26.1) is one mechanism to improve 

communication amongst the fisheries agencies. There is a need to increase 

communication with the other natural resources agencies such as the Departments 

of Transportation, Conservation, Environmental Protection and the State Planning 

Office. Task 20.1.5 is a mechanism to increase communication about connectivity 

and passage issues. 

29.7. Develop a strategy to document land use changes in the Penobscot 

River 

Connecting land use changes to potential changes in habitat quality within the river 

system and understanding how those changes affect aquatic resources is important. 

30.1. Participate in the Diadromous Species Restoration Research Network 

DSRRN, a collaborative effort to catalyze science, resource management, and 

outreach, in 2008 kick off a five year, NSF-funded networking effort focused on the 

study of questions fundamental to diadromous fish ecology and restoration. The 

strength of this project is its integration with the Penobscot River Restoration Project 

(Maine), the most ambitious restoration effort ever proposed for a watershed of this 

size. The Penobscot River Restoration Project has the potential to restore a diverse 

community of fishes with important commercial and recreational value. A project of 

this size has numerous stakeholders, including local towns and cities, non-profit 

organizations, an Indian tribe, state and federal agencies and academics. A critical 

objective of the Network is to facilitate and encourage constructive interactions 

between local, regional and international diadromous fish scientists and the local 

stakeholders with the ultimate goal of promoting state-of-the-art scientific 

approaches to multiple species restoration on a watershed scale. The DSRRN will 

conduct a series of science meetings, workshops and local networking to 

accomplish these goals, and invite the participation of any member of the ecological 

PRFP Page 113

community interested in the restoration of diadromous fishes in the context of river 

and watershed restoration. 

30.2. Examine levels of marine derived and terrestrially derived nutrients, and 

macroinvertabrate and fish communities. 

In riverine ecosystems, there is a need to examine the interactions among abiotic 

and biotic components throughout the entire basin. The aim is to eliminate or 

mitigate the causes of degraded ecological processes. A whole system view is 

required, however, because of the complexity of interactions between the upland 

and the aquatic environment, as well interactions between species. 

30.3. Examine role of climate change in altering ecosystem function and 

diadromous fish species population dynamics 

There is a need to assess how the river has changed over time. Ecosystem 

components that changed with European settlement of the Penobscot basin include: 

the fish community (introduced non-native species, lost diadromous species), 

aquatic mammals (otter, beaver), predator-prey complexes (fish, birds, and 

mammals) in physical habitat, hydrology, and riparian vegetation. Further, the role of 

climate change in altering ecosystem function and the decline of Atlantic salmon 

need to be explored, as well as the potential benefit to other species such as striped 

bass. 

30.4. Participate in the Penobscot River Science Steering Committee 

The Penobscot River Science Steering Committee was organized by the University 

of Maine’s Mitchell Center and Penobscot River Restoration Trust to organize and 

oversee scientific research and monitoring related to the restoration project. 

Members of the fisheries subcommittee include representatives from the Maine 

Department of Marine Resources, Maine Department of Environmental Protection, 

Maine Department of Inland Fisheries and Wildlife, University of Maine, U.S. Fish 

and Wildlife Service, and NOAA’s National Marine Fisheries Service. 

30.5. Examine the role of connectivity among main stems and tributaries and 

habitat types (rapids, flat waters, runs, riffles, pools), on productivity 

The recovery of the Penobscot River for all species needs to be approached 

holistically. A further understanding the ecosystem and the role of connectivity 

among main stems and tributaries and habitat types (rapids, flat waters, runs, riffles, 

pools), of marine derived and terrestrially derived nutrients, and of the 

macroinvertabrate and fish communities is needed. 

PRFP Page 114

Appendices 

Appendix A - Role of Hatchery Releases or Exogenous Stock Transfers in Alosine 

Restoration 

Appendix B - Viability of Salmon Sub-Populations by Reach in the Penobscot Basin 


Production Potential 

Appendix D - Adaptive Management Guidance for Fisheries Management in the 

Penobscot Basin 

Appendix E - Atlantic Salmon Fisheries Management Options and Strategies 

Appendix F - Atlantic Salmon Strategic Objectives 

Appendix G - Habitat Survey and Assessment Plan for the Penobscot Basin 

Appendix H - Developing a Sampling Plan for the Penobscot Basin 

Appendix I – Downstream Passage Studies for Atlantic Salmon 

Appendix J – Northern Pike Risk Assessment 

Appendix K – Northern Pike Movement Barrier Risk Assessment Survey 

PRFP Page 115

Appendix A - Role of Hatchery Releases or Exogenous Stock Transfers in 

Alosine Restoration 

Authors: Fred Seavey (USFWS) and Gail Wippelhauser (MDMR) 

1. Introduction 

The State of Maine has identified a goal of rebuilding American shad, blueback 

herring and alewife (collectively referred here as alosines) populations to the 

Penobscot River (MDMR and MDIFW 2008). Here we consider whether the 

Penobscot River alosine restoration should occur by natural recovery; by 

supplementation using adult fish transfers and/or stocking of hatchery-reared 

juveniles; and whether supplementation should use lower river stocks or exogenous 

stocks. Fish transfers 18 and hatchery supplementation with fry or fingerlings 19 using 

in-basin or out-of-basin (exogenous) sources of broodstock are common restoration 

practices in Maine and elsewhere. These restoration methods are proposed for the 

Penobscot River where alosines have been extirpated from a large portion of the 

watershed or where remnant populations are currently believed to exist in small 

numbers in the lower river (the first dam is just upstream of the head-of-tide) and its 

tributaries. 

No alosine genetic investigations are currently available for the Penobscot River or 

potential Maine donor rivers to assist us in understanding how Maine’s alosine 

populations may (or may not) be structured, but two studies are either currently 

underway or planned in the near future. One focuses on American shad genetics 

along the Atlantic Coast (P. Benson, personal communication, December 3, 2008) 

and the other addresses alewife genetics in Maine (T. Willis, personal 

communication, December 2, 2008). The results from these studies will be 

considered once it is peer-reviewed and becomes available 

This review makes a judgment as to the likelihood that Penobscot River alosine 

populations may have a population structure by reviewing the literature addressing 

alosine population structure, describing the current management experience, and 

discussing the implications of each. It also provides an approach for the use of 

exogenous stock transfer or hatchery supplementation for restoring extirpated 

Penobscot River alosine stocks based on this information. 

18 

The movement, transfer and placement of gravid adults from a self-sustaining population to an area 

with an extirpated or depressed population. 

19 

The collection of eggs from gravid adults that are then fertilized, reared and released to restore an 

extirpated populations or supplement a depressed population. 

PRFP Page 116

Population Structure 

The ‘concept’ of what is meant by a population or stock is not a settled question, 

even though it is central to the fields of ecology, evolutionary biology and 

conservation biology, and no single approach has been developed to describe what 

a population represents (Waples and Gaggiotti 2006). Therefore, much judgment 

needs to be applied to decide whether and how to manage populations. This 

decision is sometimes clear when a population is either entirely isolated or panmixic. 

Most often the situation is intermediate between these two extremes, resulting in a 

continuum of population differentiation (Waples 2006). This is the case with many 

marine fish species that are widespread, highly migratory, and have a relatively high 

gene flow (Waples 1998). We approach the question of population structure by 

summarizing known investigations that were meant to either define or identify 

specific alosine stocks, by reviewing existing management experience, and by 

making a judgment on how to approach Penobscot River stock restoration for each 

species. 

Management Stock Definition 

The management of alosines in Maine must comply with the Atlantic States Marine 

Fisheries Commission’s (ASMFC) Amendment 1 to the Interstate Fishery 

Management Plan for Shad and River Herring (“Plan”, ASMFS 1999). The Plan’s 

management unit is defined as all migratory American shad, hickory shad, and river 

herring (alewife and blueback herring) stocks of the east coast of the United States. 

In the American shad stock assessment report, ASMFC (2007a) defined stock as “a 

part of a fish population with a particular migration pattern, specific spawning 

grounds, and subject to a distinct fishery.” In the river herring stock assessment 

report, ASMFC (1990) defined stocks for alewife as the river of origin. The 

management definition for a stock is discussed below for each species in the 

summary. 

2. Alewife 

Meristic/Morphology or Genetic Investigations 

Morphology and meristic characteristics are sometimes useful in segregating groups 

and describing phenotypic expressions (Waples 1991). Messieh (1977) examined 

the population structure of river herring (primarily alewife) in the Saint John River, 

New Brunswick. He found the morphology and meristic characteristics identified 

differences in various populations but also showed a high degree of overlap. The 

most significant separation was from those populations that were geographically 

distant. Messieh surmised that river herring were probably not as specific as 

American shad in homing to tributaries because of the significant overlap in river 

herring morphology and meristics. 

PRFP Page 117

Genetic studies focused on alewife differentiation using mtDNA and microsatellite 

data and often compared anadromous and landlocked forms. This section focuses 

on the results for the anadromous form. Palkovac et al. (2008) found seven 

anadromous populations in the Connecticut River were generally weakly 

differentiated from each other using mtDNA and microsatellite data (mean FST=0.038 

and 0.012, respectively) and that gene flow (Nm=3.11) did not appear to be restricted 

at the geographic scale of the study (80 km between the most distant population). 

Chilakamarri (2005) used microsatellite data to examine two populations of 

anadromous alewife in Connecticut separated by about 40 km. She found a 

moderate level of differentiation between the two populations (pairwise FST=0.058). 

Using microsatellite data, Bentzen and Paterson (2005) compared the two 

anadromous alewife populations in the Saint Croix River with populations in the 

LaHave and Gaspereau Rivers. Anadromous populations were generally weakly 

differentiated from each other within Saint Croix River (pairwise FST=0.008), weakly 

to moderately differentiated between the Saint Croix and the LaHave and 

Gaspereau River populations (pairwise FST ranged between 0.014 and 0.044), and 

moderately differentiated between the LaHave and Gaspereau Rivers (FST =0.050) 

This result is notable since the Saint Croix River was separated from the other rivers 

by hundreds of kilometers. Bentzen (personal communication, December 3, 2008) 

noted that the data indicate that alewife populations are genetically differentiated but 

that the pattern and magnitude needed to be determined through additional study. 

Several genetic studies show that introduced landlocked alewife populations are 

very greatly differentiated from anadromous populations, suggests that the 

introductions may have occurred in recent times, and demonstrate a certain amount 

of resilience of alewife life history through these successful introductions. Bentzen 

and Paterson (2006) concluded that the landlocked alewives in the St. Croix 

watershed did not arise from the sampled anadromous population but rather a 

separate introduction. Palkovac et al. (2008) suggested that landlocked populations 

from seven Connecticut lakes diverged from a common anadromous ancestor no 

longer than 5,000 years ago and as recently as 300 years ago. Ihssen and Martin 

(1992) concluded that the Great Lake population of alewife is a recent invader that 

likely originated form the Hudson-Mohawk Rivers via the Erie Canal and the New 

York Finger Lakes. These accounts are notable in that they suggest that the 

successful invasions may be recent (within the period of European settlement). 

Numerous other alewife introductions have also been documented in lakes and 

ponds of the New England and Mid-Atlantic states (Hendricks 2003). 

Management Experience 

The ASMFC is revising its management plan for alewife based upon closure of river 

herring fisheries by many Atlantic coastal states and observed declines in 

abundances (ASMFS 2008a, ASMFS 2007a). The plan recognizes that fish 

transfers may be necessary to reestablish populations that have been extirpated 

from their habitat due to dams or other factors. Fish transfers and hatchery 

PRFP Page 118

supplementation have been highly successful in re-establishing extirpated 

populations of alewife and are currently used by many states. 

Since the mid-1970s the State of Maine has successfully restored alewife runs to 

more than 30 ponds in the Royal River, Androscoggin River, Kennebec River, 

Presumpscot River, and the mid-coast region from Cape Elizabeth to Mt. Desert 

Island by sequential, exogenous stock transfers (Damariscotta fish to the Royal, 

Royal fish to the Androscoggin, Androscoggin fish to the Kennebec, Androscoggin 

and Kennebec fish to the mid-coast). The exogenous alewives have flourished in 

non-natal ponds that varied in size, depth, trophic status, resident fish community, 

distance from the ocean, and elevation. 

The best studied alewife restoration is in the Kennebec River watershed. The lack 

of fish passage at the first dam (Edwards) for almost 150 years had caused the 

extirpation of alewives from all upstream lakes and ponds. Restoration began in 

1985 when DMR stocked 3567 alewives from the Androscoggin River into a single 

lake above Edwards Dam. Stocking was expanded to six additional Kennebec lakes 

as the Androscoggin run increased, and more adult broodstock became available. 

Exogenous stocking from the Androscoggin was terminated in 1993, because the 

number of alewife returns to Edwards Dam was sufficiently large to serve as 

broodstock. Between 1993 and 1999, nine lakes above Edwards Dam and 14 

additional in-basin and out-of-basin lakes were stocked with Kennebec alewife. 

After the removal of Edwards Dam in 1999, returning alewives were able to migrate 

17 additional miles upstream. Because alewives still had no access to spawning 

habitat, DMR continued random stocking of adults into upstream lakes (i.e., adults 

not necessarily trucked to natal waters). In 2006, DMR ceased stocking five of the 

nine upstream lakes, because fish passage installation had made them accessible. 

Interim passage at Fort Halifax (fish pump) did not allow all returning alewives to be 

passed, so the total run size could not be determined. However, 500,000 to 600,000 

fish were counted (combined passing and harvest) at Fort Halifax in multiple years 

since 2002, and the run is estimated to be greater than a million fish. 

Summary 

Based on existing information, four stocks occur in the Penobscot River (above 

Veazie, Silver Lake, Souadabscook Stream and Orland River). The ASMFS has 

defined stocks for alewife as the river of origin, however the state typically manages 

alewife based on the lake or pond of origin because of its life history. The 

management definition of a stock lends support for homing of alewife to natal rivers. 

Although not extensive, the literature available on stock identification based on either 

meristic/morphology or genetic investigations indicates weak to moderate 

differentiation that may (or may not) be based on geographic distance. The results 

are consistent with homing to natal rivers but with a stray rate that appears to be 

large enough to provide effective genetic interchange between populations (the 

range of the FST values reported was 0.008 to 0.058 which would correspond with 

PRFP Page 119

etween 4 and 41 genetically effective migrants per generation using the 

approximation of FST ≈ 1/(1 + 4mNe) described in Waples (1998)). 

The use of this information for management purposes is not simple since there is a 

lack of consensus in the genetic literature as to the biological interpretation of 

relatively low levels of genetic differentiation. Delimiting the boundaries of stock 

structure is a complex matter and approaches to define stocks in cases of low 

differentiation are still under development (Waples and Gaggiotti 2006). The use of 

microsatellites and the assumptions used in the interpretation (no selection, no 

migration, randomly mating populations, temporal data) and the need for random 

samples are susceptible to error which becomes more significant for low FST values 

typical for marine species and within the range of those reported for alewife (Waples 

1998; Balloux and Lugon-Moulin 2002). In an evaluation of current methods used 

for stock definition, Waples and Gaggiotti (2006) showed that even widely accepted 

clustering tools may not accurately assign populations in less than ideal sampling 

conditions. The results of the existing investigations provides support for additional 

studies using genetic methods in Maine, yet they should not be relied upon solely to 

make management decisions in cases of low differentiation. 

Management experience in Maine and elsewhere supports the use of exogenous 

transfer of fish to restore extirpated runs. A large number of extirpated alewife runs 

have been re-established in Maine over the last three decades and appear to be 

self-sustaining. Long-term monitoring of large restoration projects (Androscoggin 

and Kennebec Rivers) have demonstrated the success of using exogenous stocks to 

initiate runs that can then be used as the source for further restoration efforts in the 

watershed. There are also numerous successful accidental or intentional alewife 

introductions in lakes and in contemporary times (several examples are included in 

the genetic literature). These introductions coupled with the management 

experience of using exogenous transfer of fish to restore runs suggest a somewhat 

resilient life history. 

The recent ASMFC planning process also recognizes that fish transfers may be 

necessary to reestablish populations that have been extirpated from their habitat due 

to dams or other factors (ASMFS 2008a, ASMFS 2007a). One of the plan’s 

management recommendations is an alosine stocking program, including 

reintroduction to the historic spawning areas, expansion of existing stock restoration 

programs, and initiation of new strategies to enhance depressed stocks. Limburg et 

al. (2007) peer reviewed the ASFMC American shad stock assessment (ASFMS 

2007a) did not raise fish transfers or hatchery supplementation as an issue, 

negatively or positively, even though these methods were identified as a significant 

component of restoration by many states. The use of exogenous fish transfers for 

alewife is a well accepted method of restoration by ASMFS and member states and 

the risk of these methods have not be identified as a significant management 

concern. 

PRFP Page 120

3. Blueback Herring 


No literature was available that focused on stock identification for blueback herring 

based on morphology and/or meristic characteristics. Bentzen and Paterson (2005) 

compared a blueback herring population from the LaHave River with anadromous 

and non-anadromous alewife populations in the Saint Croix, LaHave and Gaspereau 

Rivers. As expected (a different species), the blueback herring were found to be 

very greatly differentiated (pairwise FST ranged between 0.37 to 0.52) from the 

alewife populations. No inferences can be drawn from this study regarding blueback 

herring population structure since it was limited to one river. 


Maine has not initiated any sustained program to transfer or culture blueback herring 

so blueback herring restoration is completed through natural recovery or incidentally 

through alewife transfers. Fish transfers and culture have also not been widely used 

for blueback herring along the Atlantic Coast. The U.S. Fish and Wildlife Service in 

cooperation with the New Hampshire Fish and Game and Massachusetts Division of 

Fish and Wildlife initiated a pilot study between 2000 and 2004 that transferred small 

numbers (from 47 to 1,307 fish) of gravid blueback herring from the Connecticut 

River/Chicopee River to the Ashuelot (NH) and Westfield (MA) Rivers (J. Rowan, 

personal communication, January 12, 2009). The program was suspended in 2005 

before it could be fully evaluated because of the regional decline in the blueback and 

the difficulty in capturing the fish. The U.S. Fish and Wildlife Service’s Harrison Lake 

National Fish Hatchery has developed culture method for blueback herring and is 

currently evaluating the use of hatchery fry to restore an extirpated run at Kimages 

Creek (VA) (M. Odom, personal communication, January 13, 2009). They have 

release between 200,000 and 1,000,000 fry each year since 2005 and will be 

evaluating the pilot project in 2009. 

Summary 

No specific information is known about the stock structure, size, or spawning 

locations of blueback herring in the Penobscot River or tributaries except that a 

remnant population exists. The ASMFS has defined stocks for blueback herring as 

the river of origin and no literature is available on stock identification based on either 

meristic/morphology or genetic investigations that would refine this stock definition. 

Maine and other states along the Atlantic Coast have not initiated any sustained 

program to transfer or culture blueback herring so blueback herring restoration is 

completed through natural recovery or incidentally through alewife transfers. 

Hatchery culture and stock transfer methods for blueback herring have been 

developed but have not been fully evaluated for restoration purposes. 

PRFP Page 121

4. American Shad 

Management Stock Structure 

A peer review of the ASMFS stock assessment for shad (Limburg et al. 2007) 

confirmed the use of individual river stocks as the management unit and also 

suggested the use of assessment approaches using regional models that reflect life 

history differences in the stocks (southern, Mid-Atlantic and North Atlantic). The 

State of Maine currently manages shad stocks based on the river of origin. No 

specific information is known about the stock structure, size, or spawning locations 

of shad in the Penobscot River or tributaries except that a remnant population exists. 

Anecdotal information suggest that the remnant population is small because of the 

low frequency and number of shad documented in the Veazie Project fishway, the 

low frequency collected during past surveys, and the estimated starting populations 

in other river systems. 


Earlier work on American shad included the analysis of otoliths (Williams 1985) and 

meristic and morphometric characteristic (Melvin 1984) to assign shad from a mixedstock 

summer fishery to one of three broad regions (Canadian Atlantic, mid-US 

Atlantic, and south-US Atlantic). Later work by Melvin et al. (1992) examined 

morphology and meristic characteristics for American shad from fourteen rivers 

between Florida and Quebec. They were able to discern a south to north separation 

within four broad regions (Florida to Cape Lookout; Cape Lookout to Cape Cod; Bay 

of Fundy; and Gulf of Saint Lawrence). The separation between adjacent regions 

was less apparent than between regions more geographically distant. They were 

able to correctly classify individuals from a mixed-stock to each region with a 79 and 

89 percent correct classification. 

Genetic investigations to discriminate populations of American shad based on 

morphology, protein electrophoresis, and analysis of mitochondrial DNA (mtDNA) 

and nuclear DNA microsatellite variation have found shad populations to be only 

weakly to moderately differentiated and subject to substantial amounts of gene flow 

(Nolan et al. 2003). 

Four studies that used restriction endonuclease (RE) analysis of mitochondrial DNA 

(mtDNA) found that differences among 23 east coast shad populations occurred 

primarily as variations in the frequencies of common and shared mtDNA haplotypes 

(Bentzen et al. 1989; Nolan et al. 1991; Epifanio et al. 1995), and haplotype 

frequencies generally were temporally stable (Brown et al. 1996). Because no 

single or group of haplotypes completely discriminated river stocks or regional 

complexes, only 28 percent of individual fish could be correctly reallocated to their 

river of origin (Epifanio et al. 1995). Surprisingly, a major life history variation 

(semelparity in populations south of Chesapeake Bay and iteroparity to the north) 

was not revealed by the mtDNA analysis. In a study of three anadromous fish 

PRFP Page 122

populations, Waldman et al. (1996) use mtDNA to examine population structure of 

shad from the Connecticut, Hudson and Delaware Rivers. They found that the 

populations from these rivers were extremely diverse showing no significant 

heterogeneity in the mtDNA frequencies. They surmised that gene flow among 

neighboring American shad populations are too great to allow differentiation. 

Results were similar in studies using microsatellite DNA. Julian and Bartron (2008) 

used mtDNA and microsatellite data to examine American shad population structure 

on the Susquehanna, Delaware and Hudson Rivers. They determined that the shad 

populations in these three rivers were not significantly differentiated from each other 

because of the lack of numerous distinct haplotypes in the mtDNA and lack of 

differentiation in the microsatellite data (pairwise FST between 0.001 and 0.0026). 

However, the lack of significant population differences observed in the three rivers 

was not unexpected given the high levels of exogenous stock transfer. Waters et al. 

(2000) found that both mtDNA and microsatellite DNA were able to distinguish subtle 

differences for the Atlantic coast for populations of American shad from the James, 

Pamunkey and Hudson Rivers (FST ≈ 0.01 for certain loci and FST=0.0063 for all loci). 

Straying among these rivers (3.9 to 71.2 breeders per generation, depending on 

calculation method) was sufficient to permit only marginal population differentiation. 

These results may be conservative given that weak differentiation was detected with 

a low number of markers (5 microsatellite loci). 

Unpublished results from Bentzen (personal communication, December 3, 2008) for 

shad populations in rivers of the Bay of Fundy have shown moderate to great 

differentiation (FST values up to 0.07, or corrected for the high heterozygosity up to 

0.24). Based on this data, he believes that genetically effective straying in shad 

must be very low. 

Waters et al. (2000) also compared an introduced, non-native shad population from 

the Columbia River (OR, WA) to the Hudson River stock, its source population. 

Their study found that the Columbia River population was highly differentiated from 

the Atlantic Coast populations. Shad is a recent invader to the Columbia River, 

introduced in the late 19 th century. Rottiers et al. (1992) noted significant differences 

in the growth and behavior and temperature and salinity tolerance of juvenile shad 

from the Columbia and Delaware Rivers. The Columbia River fish grew significantly 

faster, attained a greater final weight, and had lower mortalities at all the test 

salinities and temperatures than the Delaware River fish. This example suggests 

that changes to the shad population structure may occur relatively soon (within 20 

generations) after an introduction. 


A number of states currently use or have used exogenous fish transfers and/or 

hatchery supplementation to restore American shad (ASMFC 1999; ASMFC 2007a; 

Hendricks 2003). This management practice is well established and is incorporated 

in the ASMFC definition for restoration (ASMFC 2007a). In the New England states, 

PRFP Page 123

Maine, New Hampshire, Massachusetts and Rhode Island have used fish transfers 

or hatchery supplementation for shad with most fish originating from the Merrimack 

or Connecticut Rivers. In the Mid-Atlantic states, shad restoration has primarily 

focused in the Susquehanna River and the tributaries to the Chesapeake Bay, which 

include both fish transfers and hatchery supplementation through federal and state 

programs in New York, Pennsylvania, Maryland, and Virginia. Delaware, Hudson 

and Connecticut River shad stocks were used in the Susquehanna River restoration 

efforts. New Jersey also has conducted a stocking program in the Raritan River. 

The South Atlantic states do not have alosine restoration programs that involve fish 

transfers or hatchery supplementation except for North Carolina, which has stocked 

shad into the Roanoke River. The most recent account of these activities is included 

in ASMFC (2008b) and documents the hatchery supplementation of over 22 million 

shad in seven states and 12 rivers. 

Shad are known to be present in 9 rivers in Maine, however active restoration is 

occurring only in the Saco, Androscoggin and Kennebec Rivers (Lary 1999; ASMFC 

2007a for a full account on the status of shad in Maine). A multi-government 

strategic plan was developed for shad restoration on the Penobscot River in 2001, 

however few measures were ever implemented from the plan because of the lack of 

resources except for the group’s work in initiating the multiparty settlement 

agreement to improve fish passage (FWS et al. 2001). Restoration is currently 

achieved through natural recovery in the Saco River and Narraguagus River. 

Restoration in the Kennebec and Androscoggin includes fish transfers and/or 

hatchery supplementation. These restoration efforts were initiated in the mid-1980s 

and primarily use exogenous stocks from the Connecticut and Merrimack, although 

the Cathance and Narraguagus River stocks were also used on a very limited basis. 

In the Androscoggin River a total of 5,374 and 2,234 adult fish have been transferred 

since 1985 from the Connecticut and Merrimack Rivers, respectively. Hatchery 

supplementation has occurred since 1999 with a total of 4.8 million larvae released 

of a primarily Merrimack River origin. In the Kennebec River a total of 7,420 adult 

fish have been transferred from the Connecticut River since 1988. Hatchery 

supplementation has occurred since 1992 with a total of 30 million larvae released 

primarily Merrimack River. 

The primary management challenge when restoring shad through fish transfers 

and/or hatchery supplementation is obtaining fish from donor sources. The sources 

of broodstock for Maine are limited because of the low population size in most Maine 

Rivers; difficulty in collecting fish at fishways because they are poorly functioning 

(Brunswick Project fishway) or they have recently been constructed (Benton Falls 

and Lockwood Projects); and/or that the shad numbers are used as management 

triggers to construct future upstream fishways so there is a reluctance to use those 

stocks for supplementation (Kennebec River). Donor sources currently available to 

Maine that are of sufficient population size are runs in the Merrimack and 

Connecticut Rivers. 

PRFP Page 124

Summary 

No specific information is known about the stock structure, size, or spawning 

locations of American shad in the Penobscot River or tributaries except that a 

remnant population exists. The ASMFS has defined shad stocks based on the river 

of origin and this is consistent with the State of Maine’s management definition. The 

management definition of a stock reflects the harvest approach and lends support 

for homing of shad to natal rivers. 

The published literature available on stock identification based either on 

meristic/morphology or genetic investigations indicates weak to weakly moderate 

differentiation. As with alewife, these results are consistent with homing to natal 

rivers but with a stray rate that appears to be large enough to provide effective 

genetic interchange between populations (the range of the FST values reported was 

0.001 to 0.006 which would correspond with between 41 and 250 genetically 

effective migrants per generation using the approximation of FST ≈ 1/(1 + 4mNe) 

described in Waples (1998)). These results have to be interpreted very careful given 

the extensive use of exogenous fish transfers and/or hatchery supplementation of 

shad in the Mid-Atlantic and New England states. Unpublished data from Bentzen 

appears to indicate greater differentiation of shad populations in the Bay of Fundy 

and the potential that shad gene flow is much lower (a maximum of 3 genetically 

effective migrants per generation) than reported in the published literature. 

We choose to consider all of the available sources to understand how shad 

populations may (or may not) be structured. There are a number of genetic 

investigations prior to the development of methods using microsatellites and there 

appears to be a general expectation that the newer techniques will provide a 

dramatically higher resolution of stock structure. This may not be true in all cases 

and Waples (1998) cautions against drawing this general conclusion because the 

biological process (migration and genetic drift) should similarly act upon all markers. 

As discussed in the alewife section (see above), the interpretation of the genetic 

information for management purposes are not straight forward especially in cases of 

weak differentiation. This interpretation is further confounded by the lack 

concordance of the existing published literature with preliminary results from 

Bentzen. More genetic investigations are necessary to better understand the 

population structure in Maine, however they should not be relied upon solely to 

make management decisions in cases of low differentiation. 

Management experience in Maine and elsewhere supports the use of exogenous 

transfer of fish and hatchery supplementation to restore extirpated runs. These 

management methods are widespread through most of the states with shad 

restoration programs along the Atlantic Coast. Shad populations have been reestablished 

using these methods together with improved fish passage and habitat 

conditions (Merrimack, Pawcatuck, Connecticut and Susquehanna Rivers). Other 

states have identified the importance of hatchery supplementation in sustaining 

PRFP Page 125

depressed populations (ASFMC 2007a; Hendricks 2003). There has been little 

comprehensive evaluation of the hatchery programs with marked fish except for the 

well-funded programs, such as the Susquehanna River, however the general 

consensus is that these programs are beneficial and are a useful tool as part of a 

comprehensive restoration program (Hendricks 2003). 

The recent ASMFC planning process also recognizes that fish transfers may be 

necessary to reestablish populations that have been extirpated from their habitat due 

to dams or other factors (ASMFS 2008a, ASMFS 2007a). One of the plan’s 

management recommendations is an alosine stocking program, including 

reintroduction to the historic spawning areas, expansion of existing stock restoration 

programs, and initiation of new strategies to enhance depressed stocks. Limburg et 

al. (2007) peer reviewed the ASFMC American shad stock assessment (ASFMS 

2007a) did not raise fish transfers or hatchery supplementation as an issue, 

negatively or positively, even though these methods were identified as a significant 

component of restoration by many states. The use of exogenous fish transfers for 

shad is a well accepted method of restoration by ASMFS and the member states, 

and the risk of these methods has not been indentified as a significant issue in the 

planning documents. 

PRFP Page 126

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PRFP Page 129

Appendix B - Viability of Salmon Sub-Populations by Reach in the Penobscot 

Basin 

Author: Greg Mackey 

The Penobscot River basin consists of at least six sub-drainages upstream of, and 

four downstream of Veazie Dam, where at least that number of sub-populations of 

Atlantic salmon may occur. However, there is little information on the historic 

population structure in the Penobscot basin and currently the Penobscot basin is 

managed as a panmictic meta-population. However, based on geography and 

estimates of habitat quantity, coupled with theory of salmon homing and straying, it 

is reasonable to assume that sub-populations existed in the Penobscot and to plan 

to manage for restoration of such sub-populations. These sub-populations would be 

reproductively isolated, but with levels of straying that would allow gene flow and 

provide demographic stability. Defining likely sub-populations and predicting their 

viability will assist in developing management strategies and allocating limited 

resources. 

Currently, the greatest potential influences on salmon population structure in the 

Penobscot basin are the large dams (primarily hydroelectric). Their locations relative 

to major sub-drainages and the spatial distribution and quantity of salmon habitat 

define the geography of the basin for Atlantic salmon and other diadromous species. 

The two life stages of salmon that are most affected by dams are emigrating smolts 

and immigrating adults. Each dam has differing fish passage efficiencies for adults 

and mortality rates for smolts that depend in part on environmental conditions. For 

the purposes of this discussion, the inability to reach natal spawning areas 

(cumulative passage efficiencies) is treated as mortality. 

Although marine survival plays a pivotal role in salmon population dynamics, the 

freshwater environment must be able to compensate during low marine survival 

phases. McElhany et al. (2000) describe the role the freshwater environment must 

play to ensure viable salmon populations: “A viable salmonid population should 

exhibit sufficient productivity during freshwater life history stages to maintain its 

abundance at or above viable thresholds—even during poor ocean conditions. A 

population’s productivity should allow it both to exploit available habitat and exhibit a 

compensatory response at low population sizes. When spawner abundance is below 

the long-term mean, there should be a corresponding increase in per capita smolt 

production, even though such an increase may not suffice to offset declines in 

marine survival.” Understanding the freshwater productivity potential in the 

Penobscot basin will be essential to restoring salmon. 

We used a population matrix model, prior modeling results for the Penobscot 

(ASAL), locations of major dams, and related fish passage estimates, and spatial 

distribution of habitat to predict the viability of Atlantic salmon sub-populations in the 

Penobscot basin. We divided the Penobscot basin into reaches defined by dams 

and major sub-drainages (Table 1). 

PRFP Page 130

Table 1. Sub-drainage and reaches in the Penobscot Basin defined by dams. 

Upstream Downstream Upstream Downstream Length 

Stream SubDrainage Dam Reach Extent 

Extent km km 

(km) 

Lower 

Veazie to 

Mainstem Penobscot Verona Island Veazie Verona Island 48 0 48 

Lower 

Milford to 

Mainstem Penobscot Veazie Great Works Veazie 60 48 12 

Lower 


Mainstem Penobscot Veazie Milford Great Works 62 60 2 

Mid 

West Enfield West 

Mainstem Penobscot to Milford Enfield/Howland Milford 101 62 39 

Mid 

Weldon to 

Mainstem Penobscot West Enfield Weldon West Enfield 149 101 48 

Mid 

Medway to 

Mainstem Penobscot Weldon Medway Weldon 161 149 12 

Lower 

Gilman Falls 

Stillwater Penobscot to Stillwater Orono Veazie 

Orono 

(confluence 

54 48 6 

Lower 

Gilman Falls 

with 

Stillwater Penobscot to Stillwater Stillwater mainstem 58 54 4 

Lower 

Gilman Falls 

Stillwater Penobscot to Stillwater Gilman Falls 

Browns' Mill 

Stillwater 64 58 6 

Browns' Mill (Dover Foxcroft 

Piscataquis Piscataquis to Howland Lower) Howland 165 100 65 

Moosehead Moosehead Browns' Mill 

Manufacturing Manufacturing (Dover 

to Browns' (Dover Foxcroft Foxcroft 

Piscataquis Piscataquis Mill 

Upper) 

Lower) 

Moosehead 

Manufacturing 

166 165 1 

Guilford to 

(Dover 

Moosehead 

Foxcroft 

Piscataquis Piscataquis Manufacturing 


Guilford 

Upper) 180 166 14 

Piscataquis Piscataquis Headwaters Headwaters Guilford 

Confluence 

225 180 45 

Browns' Mill 

with 

Pleasant Piscataquis to Howland Headwaters Piscataquis 

Confluence 

213 132 81 

Headwaters 

with 

East Branch East Branch to Weldon Headwaters Mainstem 

Confluence 

238 160 78 


with 

Mattawamkeag Mattawamkeag West Enfield Headwaters Mainstem 275 142 133 


Confluence 

Lower 

Lowell 

with 

Passadumkeag Penobscot Tannery 

Lowell 

Lowell Tannery Mainstem 114 93 21 

Lower 

Tannery to 

Lowell 

Passadumkeag Penobscot Grand Falls Grand Falls Tannery 

Confluence 

135 114 21 

Lower 


with 

Kenduskeag Penobscot Verona Island Headwaters Mainstem 

Confluence 

98 40 58 

Lower 


with 

Souadabscook Penobscot Verona Island Headwaters Mainstem 

Confluence 

66 32 34 

Lower 


with 

Cove 

Penobscot Verona Island Headwaters Mainstem 

Confluence 

34 26 8 

Lower 


with 

Marsh 

Penobscot Verona Island Headwaters Mainstem 52 14 38 

River km measured for Verona Island (km 0) 

The portion of the basin upstream of Veazie is upstream of marine influence, while 

sub-drainages downstream of Veazie are influenced by tides and salt water. We 

PRFP Page 131

used Kenduskeag Stream as an example of a management reach downstream of all 

dams. To model the effects of dams on salmon population viability we developed 

management reaches that aggregate some of the finer-scale reaches described 

above (Table 2). For each management reach we tallied the number of dams a 

smolt or adult would have to pass, and then used fish passage efficiencies and 

mortality data to estimate the cumulative effects of the dams on the population 

dynamics. 

Dam passage input data were derived from numerous sources: 

Holbrook, 2007, assessed survival of smolts and smolt movement using ultrasonic 

telemetry. Survival rates for mainstem dams were estimated. Both hatchery and 

wild smolts were used in the study that provides the most recent and comprehensive 

estimates of smolt survival at dams in the Penobscot. The study integrated survival 

factors surrounding dams including effects of the dam itself, plus variables such as 

transit times through reservoirs and increased opportunity of predation. 

The ASAL model was used to estimate smolt survival at Mattaceunk Dam. Direct 

estimates of smolt survival at this dam were not available. This result was presented 

in a review of downstream fish passage in the Annual Report of the U.S. Atlantic 

Salmon Assessment Committee Report No. 17 – 2004 Activities. This review 

contained numerous FERC reports on fish passage and ASAL modeling results; 

however, most of this work was superseded by Holbrook, 2007. 

Adult Atlantic salmon upstream passage efficiencies were obtained from Fay, C., M. 

Bartron, S. Craig, A. Hecht, J. Pruden, R. Saunders, T. Sheehan, and J. Trial. 

2006. Status Review for Anadromous Atlantic Salmon (Salmo salar) in the United 

States. Report to the National Marine Fisheries Service and U.S. Fish and Wildlife 

Service. 294 pages. See this document for primary sources. 

Additional adult upstream passage efficiencies were derived from Beland and 

Gorsky, 2004 in Atlantic Salmon Freshwater Assessments and Research Semi- 

Annual Project Report NOAA Grant NA17FL1157 Covering the period November 1, 

2003 – April 30, 2004, Appendix A. Additional data from Gorsky, 2005, (Site Fidelity 

and the Influence of Environmental Variables on Migratory Movements of Adult 

Atlantic Salmon (Salmo salar L.) in the Penobscot River Basin, Maine Master’s 

Thesis. University of Maine. 2005) was also used to augment the passage 

efficiencies. 

Where multiple estimates existed, we used the high and low estimates as the range, 

and used the mean of these two values as the deterministic value. When both a 

range and mean passage efficiency or survival were given, we used the data as 

presented (Table 3). Although the data presented here represent a large body of 

work, there are still important gaps in the data for Atlantic salmon passage. The 

more recent PIT tag telemetry studies on adults and smolts tend to integrate 

variables surrounding dams. This can make it difficult to interpret the effect of a dam 

PRFP Page 132

itself verses mortality that may occur in spite of a dam for a given river segment. We 

tried to use values that likely represent dam effects, avoiding estimates with 

confounding factors such as suitable habitat between dams either in the mainstem 

or in tributaries. For those dams where no salmon passage data were available we 

choose passage efficiency based on best professional judgment. However, studies 

to quantify efficiencies will improve managers’ ability to guide recovery. 

Table 2. Management reaches and dams that affect sub-populations in those 

reaches: before and after the Penobscot dam removal and bypass project. 

Before Dam Removal 

Lower 

Penobscot Kenduskeag Mattawamkeag Passadumkeag 

Piscataquis 

Lower 

Piscataquis 

Upper East Branch 

Veazie Veazie -- Veazie Veazie Veazie Veazie 

Great 

Works 

Great Works 

-- Great Works Great Works Great Works Great Works 

Milford Milford -- Milford Milford Milford Milford 

Orono Orono -- Orono Orono Orono Orono 

Stillwater Stillwater -- Stillwater Stillwater Stillwater Stillwater 

Gilman 

Falls 

Gilman Falls 

-- Gilman Falls Gilman Falls Gilman Falls Gilman Falls 

-- 

West Enfield 

-- West Enfield 

Lowell 

Tannery Dam 

Howland Howland 

-- 

-- -- -- -- 

Brown's Mill 

(D-F Lower) 

Moosehead 

-- 

-- -- -- -- 

Manufacturing 

(D-F Upper) 

-- -- -- -- -- Guilford 

After Dam Removal 

Lower 

Penobscot Kenduskeag Mattawamkeag Passadumkeag 

Piscataquis 

Lower 

Piscataquis 

Upper East Branch 

Milford Milford -- Milford Milford Milford Milford 

Orono Orono -- Orono Orono Orono Orono 

Stillwater Stillwater -- Stillwater Stillwater Stillwater Stillwater 

Gilman Falls Gilman Falls -- Gilman Falls Gilman Falls Gilman Falls Gilman Falls 

-- 

West Enfield 

-- West Enfield 

Lowell 

Tannery Dam 

-- 

Brown's Mill 

(D-F Lower) 

Moosehead 

-- 

-- -- -- -- 

Manufacturing 

(D-F Upper) 

-- -- -- -- -- Guilford 

Table 3. Smolt and adult Atlantic salmon dam passage survival estimates 

Dam TribToBranch km 

km 

from 

Veazie 

Smolt Survival 

Proportion 

Smolts 

Using** low mean high source 

Veazie Penobscot-mainstem 48 0 1.00 0.96 0.98 1.00 Holbrook, 2007 

Great Works Penobscot-mainstem 60 12 0.89 0.91 0.96 1.00 Holbrook, 2007 

Milford Penobscot-mainstem 63 15 0.89 0.75 0.88 1.00 Holbrook, 2007 

Orono Penobscot-Stillwater 0.11 0.96 0.98 1.00 Holbrook, 2007* 

PRFP Page 133

Stillwater Penobscot-Stillwater 0.11 0.96 0.98 1.00 Holbrook, 2007* 

Gilman Falls Penobscot-Stillwater 0.11 0.96 0.98 1.00 Holbrook, 2007* 

Howland Piscataquis 100 52 1.00 0.71 0.84 0.96 Holbrook, 2007 

West Enfield Penobscot-mainstem 102 54 1.00 0.80 0.85 0.89 Holbrook, 2007 

Weldon 

(Mattaceunk) Penobscot-mainstem 150 102 1.00 0.90 0.90 0.90 ASAL Model 

Brown's Mill 

(D-F Lower) Piscataquis 166 118 1.00 0.91 0.96 1.00 median*** 

Moosehead 

Manufacturing 

(D-F Upper) Piscataquis 167 119 1.00 0.91 0.96 1.00 median*** 

Guilford Piscataquis 180 132 1.00 0.91 0.96 1.00 median*** 

Milo Sebec 1.00 0.91 0.96 1.00 median*** 

Sebec Sebec 1.00 0.91 0.96 1.00 median*** 

Pumpkin Hill Passadumkeag 115 67 1.00 0.91 0.96 1.00 median*** 

Frankfort Marsh 1.00 0.91 0.96 1.00 median*** 

Foss Mill Marsh 1.00 0.91 0.96 1.00 median*** 

West 

Winterport Marsh 1.00 0.91 0.96 1.00 median*** 

Dam TribToBranch km 

Adult Survival 

km 

from 

Veazie low mean high source 

Veazie Penobscot-mainstem 48 0 0.44 0.68 0.89 Status Review 

Great Works Penobscot-mainstem 60 12 0.38 0.81 0.95 Status Review 

Milford Penobscot-mainstem 63 15 0.86 0.90 1.00 Status Review 

Orono Penobscot-Stillwater 0.84 0.89 0.94 median*** 

Stillwater Penobscot-Stillwater 0.84 0.89 0.94 median*** 

Gilman Falls Penobscot-Stillwater 0.84 0.89 0.94 median*** 

Beland and 

Howland Piscataquis 100 52 0.84 0.89 0.93 Gorsky, 2004 

Beland and 

West Enfield 

Weldon 

Penobscot-mainstem 102 54 0.84 0.89 0.94 Gorsky, 2004 

(Mattaceunk) 

Brown's Mill 

Penobscot-mainstem 150 102 0.84 0.89 0.94 median* 

(D-F Lower) 

Moosehead 

Manufacturing 

Piscataquis 166 118 0.84 0.89 0.94 median*** 

(D-F Upper) Piscataquis 167 119 0.84 0.89 0.94 median*** 

Guilford Piscataquis 180 132 0.84 0.89 0.94 median*** 

Milo Sebec 0.84 0.89 0.94 median*** 

Sebec Sebec 0.84 0.89 0.94 median*** 

Pumpkin Hill Passadumkeag 115 67 0.84 0.89 0.94 median*** 

Frankfort Marsh 0.84 0.89 0.94 median*** 

Foss Mill Marsh 0.84 0.89 0.94 median* 

West 

Winterport Marsh 0.84 0.89 0.94 median*** 

*Stillwater survival was estimated for all three dams collectively by Holbrook due to low sample sizes. Therefore, the 

survivals given for each dam are actually the collective survival. I can adjust to get the survival proportion partitions to 

sum to the collective survival. 

**The proportion using the Stillwater Branch verses mainstem. This is the average value of the 2005 and 2006 overall 

mean usage from Holbrook, 2007. 

***No data. Median value of other dams used. 

PRFP Page 134

We estimated cumulative dam mortalities for each migratory route for both smolts 

and adults. For smolts we used data from Holbrook (2007) that estimated the 

proportion of smolts choosing to migrate down the mainstem Penobscot as opposed 

to using the Stillwater Branch. We then used these cumulative mortalities to 

calculate life stage specific monthly survivals and applied this additional monthly 

mortality to life stage specific monthly mortalities. These survivals were then used 

as parameters in a population matrix model (Robertson 2005, Sweka 2008) that 

estimated the population growth rate (lambda) as well as projected population size. 

We then compared these results to a reach without dam-related mortality. We did 

not consider amount or productivity of rearing habitat in the reaches, although we 

present data from Rago (1986) that do. The purpose of this exercise was to 

evaluate the effect of dams on the population dynamics of the sub-populations. We 

also ran scenarios under optimistic marine survival conditions, where marine survival 

was set in the model to obtain a stable population (lambda = 1), and then damrelated 

mortality was inflicted on the population. This allowed us to estimate the 

affects of the dams under ocean conditions that should otherwise allow viable subpopulations. 

The cumulative effect of dam mortality varied across management reaches in the 

Penobscot basin before and after the Penobscot Project dam removal and bypass 

(referred to as “dam removal” from here on) (Figure 1). We assumed that the 

Howland bypass will be as effective as dam removal, and set dam related mortality 

to zero for this site after dam removal. Kenduskeag Stream represents a reference 

state with no dams, while the other reaches have varying numbers of dams, 

increasing with upstream distance. Note that some reaches improve more than 

others with dam removal, particularly the Lower and Upper Piscataquis. However, 

all values of lambda are well below one, indicating that all sub-populations are not 

viable under current ocean survival conditions. 

PRFP Page 135

Subdrainage 

0.73 

0.72 

0.71 

0.70 

0.69 

0.68 

0.67 

0.66 

0.65 

0.64 

0.63 

Current and Future Lambda Values for Penobscot 

Subdrainages 

Kenduskeag 

Lower Penobscot & Passadumkeag 

Piscataquis Lower 

Piscataquis Upper 

Lambda 

East Branch Mattawamkeag 

Lambda_Current 

Lambda_Future 

East Branch 

Figure 1. Changes in lambda due to cumulative dam effects on survival of smolts 

and returning adults. X-axis depicts different management reaches in the basin. Yaxis 

is lambda, the population growth rate. 

Improving ocean survival improves to the point where populations in free-flowing 

rivers are self-sustaining (Lambda = 1) with stocking held at current levels was 

modeled next (Figure 2). This scenario assumes that all stocking occurs in the 

specified reach; therefore, each reach has an equal chance of response. Habitat 

limitations are not considered. “Removed” data indicate after dam removal and 

“Current” data indicate current conditions with the dams in place. The West Enfield 

line includes returns to the Penobscot upstream to Weldon and the Mattawamkeag. 

The Piscataquis Lower predictions are for the Piscataquis between Howland and 

Dover-Foxcroft, while the Upper Piscataquis predictions include the effects of the 

additional three dams upstream of Howland after dam removal. The sub-population 

of the Lower Piscataquis has the strongest predicted response to dam removal, 

while West Enfield and Upper Piscataquis populations will likely have only modest 

changes because there remains at least one dam on their migratory route. In spite of 

dam removal, all reaches in the Penobscot basin that still have at least one dam 

show markedly lower population size than a free-flowing river. 

PRFP Page 136

Female Returns 

16000 

14000 

12000 

10000 

8000 

6000 

4000 

2000 

0 

Set Lambda = 1 under Base Conditions with Current 

Stocking Levels: Female Returns 

Returns No Dams 

West Enfield (current 

conditions) 

West Enfield (dams 

removed) 

Piscataquis Low er 

(current conditions) 

Piscataquis Low er 

(dams removed) 

Piscataquis Upper (dams 

removed) 

0 10 20 30 40 50 60 

Year 

Figure 2. Number of female returns by year under ocean survival scenario that 

produces stable populations in a free-flowing river. Before and after dam removal 

scenarios are modeled for key management reaches. Stocking held constant for all 

reaches. 

Given the results of modeling dam mortality, managers need to be able to decide if 

the productivity of a given reach can compensate for dam-related mortality and 

maintain a viable sub-population. To illustrate this, we used electrofishing juvenile 

population assessments from 2001-2007 for various reaches (Table 4). To estimate 

the required freshwater production needed to produce a viable population we set 

lambda equal to 1 for a free-flowing river by adjusting marine survival (optimistic 

ocean conditions). We then reduced smolt and adult survivals according to the dam 

survival input data for each management reach. This reduced lambda for a given 

reach. We then adjusted survival of fry stocked at 100/unit to parr stage that made 

lambda equal to 1. We used these survival increases to adjust the number of parr 

needed to overcome the dam-related mortality for each reach and compared this to 

our recent electrofishing data (Table 5). The electrofishing data are not a random 

sample of the basin, so any conclusions drawn from this may be spurious. However, 

for illustration purposes, increases in parr populations required for viable subpopulations 

under optimistic ocean survivals range for approximately 2 times in the 

PRFP Page 137

Upper Piscataquis to 30 times in the upper Penobscot. Furthermore, the required 

parr density is well within the observed range of densities for some reaches, and 

therefore may be obtainable. Clearly, variation in freshwater productivity can play an 

important role in assessing a reach’s potential to sustain a sub-population. 

However, this identifies a critical data gap. We need a spatially explicit random 

sampling scheme for juvenile salmon populations in the Penobscot basin to 

ascertain relative differences in productivity among the major management subdrainages. 

Furthermore, sampling needs to be sufficient to capture the variability of 

juvenile abundances within and among reaches. 

Table 4. Large parr densities estimated for sites within the Penobscot basin from 

2001 to 2007. 

Below 

Lower Upper Lower Upper East 

Veazie Penobscot Penobscot Piscataquis Piscataquis Branch 

n 184 4 19 20 34 27 

Density 

Mean 

0.87 0.00 0.61 1.79 8.35 1.90 

Density 

Range 

0.00-11.38 0.00-0.00 0.00-3.08 0.00-11.04 0.00-33.73 0.00-5.74 

Density sd 2.02 0.00 0.93 2.74 8.15 1.75 

Electrofishing data 2001-2007. Estimated removal density data also reported. 

Table 5. Theoretical Increases in Freshwater Survival and Parr Densities Required 

to Compensate for the Effects of Dams after the Penobscot Project Dam Removals: 

Lambda set to 1 by increasing marine survival in un-dammed scenario. 

Ratio 

increase 

needed 

relative to 

undammed 

river 

Required 

parr density 

Observed 

mean 

density 

Observed 

range 

Increase 

(multiplier) 

needed for 

replacemen 

t 

Below 

Veazie 

Lower 

Penobscot 

Upper 

Penobscot 

Lower 

Piscataquis 

Upper 

Piscataquis 

East 

Branch 

1 1.29 1.71 1.29 1.57 2.02 

10.89 14.08 18.66 14.08 17.08 22.01 

0.87 0.00 0.61 1.79 8.35 1.90 

0.00- 

11.38 

0.00-0.00 0.00-3.08 0.00-11.04 0.00-33.73 0.00-5.74 

12.52 na 30.59 7.87 2.05 11.58 

Rago (1986) modeled population segment viability in the Penobscot basin using the 

ASAL model. Mortality of both adults and smolts increased with the number of dams 

PRFP Page 138

that must be passed. Furthermore, he expressed population segment viability in 

half-lives, and showed that population viability was affected by the number of dams, 

with the Upper Piscataquis (Guilford) having the shortest half-life of 6.52 years and 

the segments with no dams or few dams (Mouth to Great Works) was self-sustaining 

(presented as 100 years). The population half-life estimates take into account 

population segment size and smolt production potential. Some parameters such as 

angling mortality have changed since 1986, and we now have updated dam survival 

data for some dams. Nevertheless, the findings from 1986 are consistent with our 

results. 

Population Segment 

Figure 3. Survival of smolts (downstream) and adults (upstream) for population 

segments defined by dams in the Penobscot Basin. Adapted from Rago (1986). 


Other Tribs 

Tribs: Mattaceunk 

Tribs: West Enfield 

Pleasant 

East Branch 

Mattawamkeag 


Upper DF 

Lower DF 

Howland 

West Enfield 

Milford 

Great Works 

Veazie 

Mouth 




Pleasant 

East Branch 

Mattawamkeag 


Upper DF 

Lower DF 

Howland 

West Enfield 


Great Works 

Veazie 

Mouth 

0.94112 

0.94112 

0.95452 

0.95452 

0.94537 

0.95569 

0.95569 

0.97589 

0.96906 

0.96906 

0.96906 

0.97589 

0.98208 

0.9925 

0.9 0.92 0.94 0.96 0.98 1 1.02 

0.00 

6.52 

Downstream Survival of Smolts 

11.73 

10.93 

8.11 

18.12 

16.39 

17.86 

15.85 

18.10 

39.82 

39.74 

1 

100.00 

100.00 

100.00 

0.00 20.00 40.00 60.00 80.00 100.00 120.00 

Expected Half-life (years) 




Pleasant 

East Branch 

Mattawamkeag 

Upper DF 

Lower DF 

West Enfield 

Great Works 

Figure 4. Population segment half-lives in years for Penobscot basin Atlantic 

salmon with marine survival rate of 0.025. Adapted from Rago (1986). 

PRFP Page 139 



Howland 


Veazie 

Mouth 

0.55785 

0.65908 

0.65908 

0.60636 

0.71639 

0.71639 

0.71639 

0.65908 

0.77869 

0.71639 

0.71639 

0.77869 

0.8464 

0.92 

0 0.2 0.4 0.6 0.8 1 1.2 

Upstream Survivial of Adults 

1

CONCLUSIONS 

Reaches where salmon must pass numerous dams are less likely to result in viable 

sub-populations. Management efforts should concentrate on reaches with fewer 

dams, balancing survival with production potential (amount and quality of available 

habitat). Where production potentials are equal, reaches with the fewest dams will 

be more likely to produce self-sustaining populations. To make these balancing 

decisions managers need estimates of freshwater production potential for all 

management reaches. They also need better fish passage efficiency and dam 

mortality estimates that will allow them to 1) improve fish passage, or 2) manage 

populations in the face of fish passage losses. 

PRFP Page 140


Production Potential 


We estimated juvenile Atlantic salmon rearing habitat in the Penobscot basin using 

both field survey data and data from a GIS-based habitat model (GIS-Based Atlantic 

Salmon Habitat Model, Draft, 2008, Appendix C, Critical Habitat). Habitat data were 

aggregated at several spatial scales within the basin, including Dam Reach, 

Management Reach, and HUC 10. The data used in this work are available as an 

ARCMap geodatabase. The goals of this work were to 1) provide the best available 

information on Atlantic salmon rearing habitat in the Penobscot basin, 2) provide an 

estimate of the relative potential for large parr production in the basin, and 3) Identify 

reaches with the highest parr production potential. 

Dam Reaches are defined as areas of the basin that are affected by a common 

collection of dams; therefore, fish in these reaches experience the same dam-related 

passage and mortality rates (Figure 1). Management Reaches attempt to organize 

the basin into reaches that could be managed independently (Figure 2). This 

provides finer scale information to managers that may be more useful for some 

management actions. The HUC system can also be used to aggregate data at any 

HUC level. Management actions may be described by these reaches, but also, finer 

scale management may be performed at the stream level. In any case, the location 

of management actions within the geographic hierarchy will be known. 

Figure 1. Dam Reaches of the Penobscot Basin 

West Branch and 

Webster Brook- 

Inaccessible 

Brown's Mill to Howland 

Headwaters to Guilford 

Guilford to Moosehead Manufacturing 

Veazie to Verona Island 

Headwaters to Weldon 

!( 

!( 

Figure 2. Management Reaches of the Penobscot Basin 

!( !( 

!( !( 

!( 

!( 

!( !( 

PRFP Page 141 

!( 

!( 

Milford to Veazie 

Medway to Weldon 

Weldon to West Enfield 

Gilman to West Lowell Tannery 

West Enfield to Milford 

Gilman to Stillwater

West Branch- 

Inaccessible 

Pleasant River 

Seboeis Stream 

Sebec River 

Piscataquis Upper 

Guilford to Moosehead 

Manufacturing 

Nesowadnehunk- 

Historically Inaccessible 

Piscataquis Lower 

Pushaw and Dead 

Pushaw Stream 

Kenduskeag 

Stillwater Gilman to Orono 

Penobscot Milford to Veazie 

Souadabscook 

!( 

Penobscot Below Veazie 

Sedgeunkedunk Stream 

Wassataquoik Stream 


Historically Inaccessible 

!( 

Marsh 

Silver Lake 

We used the quantile regression model to estimate the upper echelon of parr 

production potential based on the independent variable watershed area (Parr 

Density = [10^(1.0809-0.0006*km^2)] – 1) (Figure 3). Watershed area integrates 

many variables such as stream size, gradient, water temperature, and biological 

community composition. It is at the 90 th quantile where watershed area clearly 

functions as a limiting factor. This model uses the 90 th quantile to predict parr 

population size- that is, it predicts parr numbers based on what is observed at the 

90 th quantile of streams in Maine. Therefore, the realized parr production will usually 

be lower than predicted, but these data provide the upper threshold of parr 

production for a given watershed area. Finally, these data provide a reference to 

assess actual parr production, enabling managers to compare production to 

expectations based on the upper 90 % of streams in Maine. 

Figure 3. Quantile regression models (90 th and 75 th Quantiles) of Atlantic salmon 

parr densities verses watershed size for Maine rivers 

PRFP Page 142 

!( !( 

!( !( 

!( 

!( 

!( !( 

East Branch 

!( 

Seboeis River 

!( 

Toddy Pond 

West Branch Mattawamkeag River 

Long Pond 

Eaton Brook 

Felts Brook 

Hoyt Brook 

Hemlock Stream 

Baskahegan Stream 

Mattawamkeag 

Passadumkeag 

Olamon Stream 

Birch Stream 

Sunkhaze Stream 

Great Works Stream 

Chemo Pond 

Alamoosook Lake 

East Branch Mattawamkeag River 


Wytopitlock Stream 

Molunkus Stream 

Penobscot West Enfield to Milford

Parr density (no. / 100 m 2 ) 

45 

40 

35 

30 

25 

20 

15 

10 

5 

0 

0 200 400 600 800 1,000 1,200 1,400 1,600 

The GIS-based habitat model used slope, cumulative drainage area and 

physiographic province to predict Atlantic salmon rearing habitat throughout Maine. 

Stream widths were estimated using regional hydraulic curves for Maine rivers. We 

used the Penobscot basin portion of this dataset. We then compared reaches that 

were surveyed using field methods to the model predictions. This revealed 1) the 

model is conservative, habitat was either predicted at or below the levels observed 

in the field (Figure 4), and 2) errors in predicting stream width accounted for about 

75% of the variability in the difference between field observations and model 

predictions (Figure 5). 

Figure 4. Field verses modeled habitat data with perfect prediction reference line 

(one to one). 

Model Habitat Units 

16000 

14000 

12000 

10000 

8000 

6000 

4000 

2000 

Field verses Modeled Habitat Data- Penobscot Basin 

Field to Model 

One to One 

Cumulative drainage area (sq km) 

Linear (Field to Model) 

0 

0 2000 4000 6000 8000 10000 12000 14000 16000 

Field Survey Habitat Units 

Aroostook Dennys 

East Machias Kennebec 

Machias Narraguagus 

Pleasant Penobscot 

Saco Sheepscot 

75th Quantile 90th Quantile 

PRFP Page 143

Figure 5. Effect of stream width prediction error on estimation errors of predicted 

habitat. 

Proportional Difference in Habitat ((Field- 

Model/Field)) 

Proportional Difference in Width verses Proportional 

Differences in Habitat 

R 2 = 0.7537 

0 

-3 -2.5 -2 -1.5 -1 -0.5 0 0.5 1 1.5 

-0.5 

Table 1 presents the best current information on the amount of habitat in the 

Penobscot basin based on both the GIS model and contemporary field surveys. 

Field survey data covered only a small portion of the basin; therefore, we used the 

model data output as the primary source, and replaced modeled data with survey 

data in reaches where field survey data were available. This resulted in a data set 

comprised of modeled and observed data. The data are aggregated at the Dam, 

Management, and HUC 10 levels. Other aggregations are possible using the 

geodatabase. 

Table 1. Penobscot Basin Atlantic Salmon Habitat Data: GIS-Model Results and 

Field Survey Combined 

Habitat in units (100 m^2) 

Model 

(surveyed 

Management 

reaches 

Total 

Dam Reach Reach HUC 10 NAME 

subtracted) Survey Habitat 

Headwaters 

East Branch Penobscot 

to Weldon East Branch River (2) 5173 6967 12140 

Headwaters 

East Branch Penobscot 

to Weldon 

Headwaters 

East Branch River (3) 8244 8244 


Headwaters 

East Branch Grand Lake Matagamon 5740 5740 

to Weldon Seboeis River Seboeis River 6108 7442 13550 

Headwaters Wassataquoik East Branch Penobscot 

to Weldon Stream 

River (3) 4537 4855 9393 

Total Habitat 29802 19264 49067 


West Mattawamkeag Mattawamkeag River (1) 2115 2480 4595 

PRFP Page 144 

1.5 

1 

0.5 

-1 

-1.5 

-2 

-2.5 

Proportional Difference in Width ((Field-Model/Field)) 

-3

Enfield 


West 

Enfield Mattawamkeag Mattawamkeag River (2) 3960 2122 6083 


West 

Enfield Mattawamkeag Mattawamkeag River (3) 2286 5133 7419 


West 

Enfield Mattawamkeag 


West 

Enfield 


West 

Enfield 


West 

West Branch 

Mattawamkeag 

River 

East Branch 

Mattawamkeag 

River 



West 



West 

Enfield 

Headwaters 

to Guilford 


Moosehead 

Manufacturi 

ng 

West Branch 

Mattawamkeag River 639 639 

West Branch 

Mattawamkeag River 9184 2174 11359 

East Branch 

Mattawamkeag River 3660 1059 4719 

Penobscot River (1) at 

Mattawamkeag 9045 9045 


West Enfield 6970 6970 

Molunkus 

Stream Molunkus Stream 4517 4517 

Total Habitat 42377 12968 55345 

Piscataquis 

Upper Piscataquis River (1) 15550 3287 18836 


Moosehead 

Manufacturing Piscataquis River (3) 1286 1204 2490 

Brown's Mill Piscataquis 

to Howland Lower Piscataquis River (3) 2260 1862 4122 

Brown's Mill Piscataquis 

to Howland 

Brown's Mill 

Lower Piscataquis River (4) 3556 14815 18371 


Brown's Mill 

Pleasant River Pleasant River 19656 4298 23954 


Brown's Mill 

Sebec River Sebec River 15648 15648 

to Howland Seboeis Stream Seboeis Stream 5516 5516 

Total Habitat 46636 20975 67611 


West 

Enfield 


West 

Enfield 

Wytopitlock 

Stream Mattawamkeag River (2) 833 833 

Baskahegan 

Stream Baskahegan Stream 3789 3789 

Total Habitat 4621 4621 

PRFP Page 145

Gilman to 

West Lowell 

Tannery Passadumkeag Passadumkeag River 7950 7950 


Stillwater Pushaw Stream Pushaw Stream 5447 5447 


Weldon 

West 

Enfield to 



Weldon 

Penobscot West 

Enfield to Milford 


Mattawamkeag 1391 1391 


Orson Island 4866 4866 

West 


Milford Birch Stream Birch Stream 1078 1078 

West 


Milford Birch Stream Sunkhaze Stream 582 582 

West 


Milford Hemlock Stream 

West 


Milford Hoyt Brook 





West 


Milford Olamon Stream Olamon Stream 1424 1424 

West 



Sunkhaze 

Stream Sunkhaze Stream 1453 1453 

Total Habitat 10126 10126 

The relationship between stream width and distribution of both habitat and parr 

production potential is presented in figure 7. Parr production potential is highest in 

streams less than 12 m wide, with streams in the 4-6 m size class producing more 

parr than other stream class. Parr production in streams over 100 m wide (3665 

km^2 drainage area) were forced to zero in 45 of 52,049 stream segments because 

these streams exceeded the range of the model and produced negative parr 

estimates. This strongly suggests that stocking fry in streams 4 to 12 m wide will 

produce the most parr. Complete habitat amounts by stream width and basin 

geography are presented in Table 2. 

PRFP Page 146

Habitat (units) 

Parr Production 



Figure 7. Atlantic salmon habitat and parr production by stream width in the 

Penobscot basin (gray dashes indicate no observations) 

16,000 

14,000 

12,000 

10,000 

8,000 

6,000 

4,000 

2,000 

0 

Habitat: Headw aters to Guilford 

0-2 

6-8 

12-14 

18-20 

24-26 

30-32 

36-38 

42-44 

48-50 

75,000 

60,000 

45,000 

30,000 

15,000 

0 

Parr Production: Headw aters to Guilford 

0-2 

6-8 

12-14 

18-20 

24-26 

30-32 

16,000 

14,000 

12,000 

10,000 

8,000 

6,000 

4,000 

2,000 

0 

75,000 

60,000 

45,000 

30,000 

15,000 

0 

36-38 

Stream Width (m) 

Habitat: Mattaw amkeag River 

42-44 

Parr Production: Mattaw amkeag River 


48-50 





16,000 

14,000 

12,000 

10,000 

8,000 

6,000 

4,000 

2,000 

0 

Habitat: Brow n's Mill to How land 

0-2 

6-8 

12-14 

18-20 

24-26 

30-32 

75,000 

60,000 

45,000 

30,000 

15,000 

0 

PRFP Page 147 

36-38 

42-44 

Parr Production: Brow n's Mill to How land 

0-2 

6-8 

12-14 

18-20 

24-26 

30-32 

36-38 

42-44 

48-50 

16,000 

14,000 

12,000 

10,000 

8,000 

6,000 

4,000 

2,000 

0 

75,000 

60,000 

45,000 

30,000 

15,000 

0 


Habitat: West Branch Mattaw amkeag River 

48-50 

Parr Production: West Branch Mattaw amkeag 






16,000 

14,000 

12,000 

10,000 

8,000 

6,000 

4,000 

0-2 

6-8 

12-14 

18-20 

24-26 

30-32 

2,000 

0 

75,000 

60,000 

45,000 

30,000 

0-2 

6-8 

12-14 

18-20 

24-26 

30-32 

15,000 

0 

16,000 

14,000 

12,000 

10,000 

8,000 

6,000 

4,000 

2,000 

0 

75,000 

60,000 

45,000 

Habitat: Pleasant River 

36-38 

Parr Production: Pleasant River 

36-38 


42-44 

42-44 

Habitat: East Branch Mattaw amkeag River 

0-2 

6-8 

12-14 

18-20 

24-26 

30-32 

36-38 

0-2 

42-44 

6-8 

48-50 

12-14 

18-20 

24-26 

30-32 

0-2 

36-38 

6-8 

42-44 

12-14 

48-50 

18-20 

24-26 

30-32 

36-38 

0-2 

42-44 

6-8 

48-50 

12-14 

18-20 

24-26 

30-32 

0-2 

36-38 

6-8 

42-44 

12-14 

48-50 

18-20 

24-26 

30-32 

36-38 

0-2 

42-44 

6-8 

48-50 

12-14 

18-20 

24-26 

30-32 

36-38 

42-44 

48-50 

30,000 

15,000 

0 

48-50 

48-50 

Parr Production: East Branch Mattaw amkeag 

Stream Width (m)



16,000 

14,000 

12,000 

10,000 

8,000 

6,000 

4,000 

2,000 

0 

75,000 

60,000 

45,000 

30,000 

15,000 

0 

16,000 

14,000 

12,000 

10,000 

8,000 

6,000 

4,000 

2,000 

0 

Habitat: East Branch 

Parr Production: East Branch 


Habitat: Souadabscook 

0-2 

6-8 

12-14 

18-20 

24-26 

30-32 

36-38 

0-2 

42-44 

6-8 

48-50 

12-14 

18-20 

24-26 

30-32 

36-38 

42-44 

48-50 

0-2 

6-8 

12-14 

18-20 

24-26 

30-32 

36-38 

42-44 

48-50 



75,000 

60,000 

45,000 

30,000 

15,000 

0 

Parr Production: Souadabscook 




16,000 

14,000 

12,000 

10,000 

8,000 

6,000 

4,000 

2,000 

0 

75,000 

60,000 

45,000 

30,000 

15,000 



0 

16,000 

14,000 

12,000 

10,000 

8,000 

6,000 

4,000 

2,000 

Habitat: Wassataquoik Stream 

Parr Production: Wassataquoik Stream 

0 

75,000 

60,000 

45,000 

30,000 

15,000 

0 

0-2 

6-8 

12-14 

18-20 

24-26 

30-32 

36-38 

0-2 

42-44 

6-8 

48-50 

12-14 

18-20 

24-26 

30-32 

0-2 

36-38 

6-8 

42-44 

12-14 

48-50 

18-20 

24-26 

30-32 

36-38 

0-2 

42-44 

6-8 

48-50 

12-14 

18-20 

24-26 

30-32 

0-2 

36-38 

6-8 

42-44 

12-14 

48-50 

18-20 

24-26 

30-32 

36-38 

0-2 

42-44 

6-8 

48-50 

12-14 

18-20 

24-26 

30-32 

36-38 

42-44 

48-50 


Habitat: Kenduskeag 

0-2 

6-8 

12-14 

18-20 

24-26 

30-32 

36-38 

42-44 

48-50 

Parr Production: Kenduskeag 


Habitat: Sebois River 

We queried stream width in the Penobscot basin to illustrate the stream segments to 

stock that will optimize parr production (figure 8). Concentrating fry stocking in 

stream 4 to 12 m in width should yield greater numbers of parr than stocking other 

size streams. This exercise resulted in 57,095 units of optimal fry stock habitat 

(segments >50% rearing habitat), or the requirement of over 5 million fry to seed the 

habitat at 100 fry/unit. In addition, there were another 22,961 units in segments with 

less than 50 % habitat, for a total of 80,056 units. With the Penobscot fry production 

currently around one million, management decisions will be required as to where to 

stock fry. More detailed optimizations could be carried out to address specific 

management concerns. In addition, juvenile population assessment data may reveal 

stream reaches larger than 12 m in width that outperform expectations and should 

be considered for stocking. However, this should be done so based on data, and 

lacking such information, using the 4 to 12 m width recommendation is a sound first 

step. 

PRFP Page 148 



16,000 

14,000 

12,000 

10,000 

8,000 

6,000 

4,000 

2,000 

0 

75,000 

60,000 

45,000 

30,000 

15,000 



0 

16,000 

14,000 

12,000 

10,000 

8,000 

6,000 

4,000 

2,000 

0 

75,000 

60,000 

45,000 

30,000 

15,000 

0 

Parr Production: Sebois River 


Habitat: Passadumkeag 

Parr Production: Passadumkeag 

0-2 

6-8 

12-14 

18-20 

24-26 

30-32 

36-38 

0-2 

42-44 

6-8 

48-50 

12-14 

18-20 

24-26 

30-32 

36-38 

42-44 

48-50 

Stream Width (m)

Figure 8. Optimal parr production stocking segments in the Penobscot basin 

Red=~50-100 % rearing, Orange = ~0-50 % rearing 



Inaccessible 






!( 

!( 

Stocking various life stages should be tailored to this information. Egg and fry 

stocking are most likely to benefit from smaller stream (width

Table 2. Penobscot basin Atlantic salmon habitat (GIS-model) and predicted 90 th quantile large parr production 

Subwatershed Dam Reach Management Reach 

PRFP Page 150 

Width 

Class (m) Rearing Units 

Large Parr 

Production 

Piscataquis Headwaters to Guilford Piscataquis Upper 0 to 2 1,384 15,269 


Piscataquis Headwaters to Guilford Piscataquis Upper 4 to 6 996 10,833 














Headwaters to Guilford Total 18,914 180,139 

Piscataquis Upper Total 18,914 180,139 

Piscataquis Guilford to Moosehead Manufacturing Guilford to Moosehead Manufacturing 0 to 2 294 3,245 




Piscataquis Guilford to Moosehead Manufacturing Guilford to Moosehead Manufacturing 8 to 10 56 588 






Guilford to Moosehead Manufacturing Total 2,660 17,943 

Guilford to Moosehead Manufacturing Total 2,660 17,943 

Piscataquis Brown's Mill to Howland Piscataquis Lower 0 to 2 377 4,157 

Piscataquis Brown's Mill to Howland Piscataquis Lower 2 to 4 2,254 24,770 



Piscataquis Brown's Mill to Howland Piscataquis Lower 8 to 10 499 5,227


PRFP Page 151 

Width 


Large Parr 

Production 






Piscataquis Lower Total 16,549 69,218 

Piscataquis Brown's Mill to Howland Pleasant River 0 to 2 811 8,941 

Piscataquis Brown's Mill to Howland Pleasant River 2 to 4 6,427 70,663 











Piscataquis Brown's Mill to Howland Pleasant River 24 to 26 103 759 





Pleasant River Total 21,288 205,576 

Piscataquis Brown's Mill to Howland Sebec River 0 to 2 1,207 13,313 




Piscataquis Brown's Mill to Howland Sebec River 8 to 10 750 7,849 







Piscataquis Brown's Mill to Howland Sebec River 22 to 24 345 2,752


PRFP Page 152 

Width 


Large Parr 

Production 





Sebec River Total 15,648 147,102 

Piscataquis Brown's Mill to Howland Seboeis Stream 0 to 2 74 815 

Piscataquis Brown's Mill to Howland Seboeis Stream 2 to 4 1,420 15,590 

Piscataquis Brown's Mill to Howland Seboeis Stream 4 to 6 557 6,054 








Piscataquis Brown's Mill to Howland Seboeis Stream 24 to 26 1,069 8,144 




Seboeis Stream Total 5,516 49,288 

Brown's Mill to Howland Total 59,001 471,184 

Piscataquis Total 80,574 669,266 

East Branch Headwaters to Weldon East Branch 0 to 2 83 911 

East Branch Headwaters to Weldon East Branch 2 to 4 5,844 64,275 



East Branch Headwaters to Weldon East Branch 8 to 10 337 3,531 







East Branch Total 22,242 147,125


PRFP Page 153 

Width 


Large Parr 

Production 

East Branch Headwaters to Weldon Seboeis River 0 to 2 18 200 

East Branch Headwaters to Weldon Seboeis River 2 to 4 2,679 29,462 

East Branch Headwaters to Weldon Seboeis River 4 to 6 456 4,944 












Seboeis River Total 7,448 67,935 

East Branch Headwaters to Weldon Wassataquoik Stream 0 to 2 38 420 

East Branch Headwaters to Weldon Wassataquoik Stream 2 to 4 2,672 29,395 

East Branch Headwaters to Weldon Wassataquoik Stream 4 to 6 388 4,234 




East Branch Headwaters to Weldon Wassataquoik Stream 12 to 14 83 822 


East Branch Headwaters to Weldon Wassataquoik Stream 26 to 28 1,140 8,000 

Wassataquoik Stream Total 5,790 57,767 

Headwaters to Weldon Total 35,480 272,827 

East Branch Total 35,480 272,827 

Mattawamkeag Weldon to West Enfield Baskahegan Stream 0 to 2 112 1,228 

Mattawamkeag Weldon to West Enfield Baskahegan Stream 2 to 4 1,645 18,085 


Mattawamkeag Weldon to West Enfield Baskahegan Stream 6 to 8 89 954 




Mattawamkeag Weldon to West Enfield Baskahegan Stream 20 to 22 188 1,551


PRFP Page 154 

Width 


Large Parr 

Production 




Baskahegan Stream Total 3,789 32,606 

Mattawamkeag Weldon to West Enfield East Branch Mattawamkeag River 0 to 2 40 442 

Mattawamkeag Weldon to West Enfield East Branch Mattawamkeag River 2 to 4 2,026 22,271 

Mattawamkeag Weldon to West Enfield East Branch Mattawamkeag River 4 to 6 445 4,843 








East Branch Mattawamkeag River Total 3,973 40,680 

Mattawamkeag Weldon to West Enfield Mattawamkeag 0 to 2 340 3,751 

Mattawamkeag Weldon to West Enfield Mattawamkeag 2 to 4 6,692 73,572 








Mattawamkeag Weldon to West Enfield Mattawamkeag 20 to 22 39 327 


Mattawamkeag Weldon to West Enfield Mattawamkeag 40 to 42 122 511 

Mattawamkeag Weldon to West Enfield Mattawamkeag 50 to 300 15,410 0 

Mattawamkeag Total 33,176 187,081 

Mattawamkeag Weldon to West Enfield Molunkus Stream 2 to 4 2,531 27,840 

Mattawamkeag Weldon to West Enfield Molunkus Stream 4 to 6 445 4,831 



Mattawamkeag Weldon to West Enfield Molunkus Stream 10 to 12 10 105


PRFP Page 155 

Width 


Large Parr 

Production 

Mattawamkeag Weldon to West Enfield Molunkus Stream 12 to 14 95 945 


Mattawamkeag Weldon to West Enfield Molunkus Stream 24 to 26 58 432 



Molunkus Stream Total 4,517 45,329 

Mattawamkeag Weldon to West Enfield West Branch Mattawamkeag River 0 to 2 67 738 

Mattawamkeag Weldon to West Enfield West Branch Mattawamkeag River 2 to 4 3,715 40,848 


Mattawamkeag Weldon to West Enfield West Branch Mattawamkeag River 6 to 8 892 9,527 












West Branch Mattawamkeag River Total 10,651 100,973 

Mattawamkeag Weldon to West Enfield Wytopitlock Stream 2 to 4 490 5,384 



Mattawamkeag Weldon to West Enfield Wytopitlock Stream 16 to 18 10 97 

Wytopitlock Stream Total 833 8,960 

Weldon to West Enfield Total 56,938 415,629 

Mattawamkeag Total 56,938 415,629 

Lower Penobscot Medway to Weldon Medway to Weldon 0 to 2 26 292 

Lower Penobscot Medway to Weldon Medway to Weldon 2 to 4 855 9,397 

Lower Penobscot Medway to Weldon Medway to Weldon 4 to 6 317 3,439 


Lower Penobscot Medway to Weldon Medway to Weldon 8 to 10 14 146


PRFP Page 156 

Width 


Large Parr 

Production 




Medway to Weldon Total 1,391 15,007 

Medway to Weldon Total 1,391 15,007 

Lower Penobscot West Enfield to Milford Birch Stream 0 to 2 52 578 

Lower Penobscot West Enfield to Milford Birch Stream 2 to 4 443 4,873 








Birch Stream Total 1,660 17,378 

Lower Penobscot West Enfield to Milford Hemlock Stream 0 to 2 112 1,236 


Lower Penobscot West Enfield to Milford Hemlock Stream 4 to 6 13 137 



Hemlock Stream Total 447 4,799 

Lower Penobscot West Enfield to Milford Hoyt Brook 2 to 4 212 2,328 

Lower Penobscot West Enfield to Milford Hoyt Brook 8 to 10 63 660 

Hoyt Brook Total 275 2,988 

Lower Penobscot West Enfield to Milford Olamon Stream 0 to 2 15 168 

Lower Penobscot West Enfield to Milford Olamon Stream 2 to 4 476 5,221 






Olamon Stream Total 1,424 14,727


PRFP Page 157 

Width 


Large Parr 

Production 

Lower Penobscot West Enfield to Milford Penobscot West Enfield to Milford 0 to 2 46 508 

Lower Penobscot West Enfield to Milford Penobscot West Enfield to Milford 2 to 4 247 2,718 





Lower Penobscot West Enfield to Milford Penobscot West Enfield to Milford 50 to 300 4,070 388 

Penobscot West Enfield to Milford Total 4,866 8,125 

Lower Penobscot West Enfield to Milford Sunkhaze Stream 0 to 2 15 170 

Lower Penobscot West Enfield to Milford Sunkhaze Stream 2 to 4 527 5,783 





Lower Penobscot West Enfield to Milford Sunkhaze Stream 12 to 14 43 433 

Sunkhaze Stream Total 1,453 15,554 

West Enfield to Milford Total 10,126 63,571 

Lower Penobscot Milford to Veazie Chemo Pond 2 to 4 402 4,417 

Lower Penobscot Milford to Veazie Chemo Pond 4 to 6 25 267 



Lower Penobscot Milford to Veazie Chemo Pond 10 to 12 16 162 

Chemo Pond Total 691 7,483 

Lower Penobscot Milford to Veazie Great Works Stream 0 to 2 12 131 

Lower Penobscot Milford to Veazie Great Works Stream 2 to 4 504 5,536 





Great Works Stream Total 951 10,247 

Lower Penobscot Milford to Veazie Penobscot Milford to Veazie 0 to 2 2 24 

Lower Penobscot Milford to Veazie Penobscot Milford to Veazie 2 to 4 111 1,216 

Lower Penobscot Milford to Veazie Penobscot Milford to Veazie 4 to 6 120 1,312


PRFP Page 158 

Width 


Large Parr 

Production 

Lower Penobscot Milford to Veazie Penobscot Milford to Veazie 16 to 18 24 224 

Lower Penobscot Milford to Veazie Penobscot Milford to Veazie 50 to 300 9,822 0 

Penobscot Milford to Veazie Total 10,080 2,776 

Lower Penobscot Milford to Veazie Stillwater Gilman to Orono 2 to 4 35 381 

Lower Penobscot Milford to Veazie Stillwater Gilman to Orono 40 to 42 1,646 6,764 

Stillwater Gilman to Orono Total 1,681 7,145 

Milford to Veazie Total 13,402 27,651 

Lower Penobscot Gilman to Stillwater Pushaw Stream 0 to 2 455 5,014 

Lower Penobscot Gilman to Stillwater Pushaw Stream 2 to 4 1,627 17,883 





Lower Penobscot Gilman to Stillwater Pushaw Stream 12 to 14 78 770 






Pushaw Stream Total 5,447 56,483 

Gilman to Stillwater Total 5,447 56,483 

Lower Penobscot Gilman to West Lowell Tannery Passadumkeag 0 to 2 203 2,252 

Lower Penobscot Gilman to West Lowell Tannery Passadumkeag 2 to 4 2,338 25,704 




Lower Penobscot Gilman to West Lowell Tannery Passadumkeag 10 to 12 88 903 







Lower Penobscot Gilman to West Lowell Tannery Passadumkeag 36 to 38 825 3,963


PRFP Page 159 

Width 


Large Parr 

Production 



Passadumkeag Total 7,950 66,620 

Gilman to West Lowell Tannery Total 7,950 66,620 

Lower Penobscot Veazie to Verona Island Alamoosook Lake 0 to 2 97 1,071 



Lower Penobscot Veazie to Verona Island Alamoosook Lake 6 to 8 61 660 




Alamoosook Lake Total 848 9,051 

Lower Penobscot Veazie to Verona Island Eaton Brook 2 to 4 39 422 



Lower Penobscot Veazie to Verona Island Eaton Brook 10 to 12 107 1,097 

Eaton Brook Total 276 2,918 

Lower Penobscot Veazie to Verona Island Felts Brook 2 to 4 40 445 

Lower Penobscot Veazie to Verona Island Felts Brook 4 to 6 30 321 

Lower Penobscot Veazie to Verona Island Felts Brook 6 to 8 139 1,478 

Felts Brook Total 209 2,244 

Lower Penobscot Veazie to Verona Island Kenduskeag 0 to 2 260 2,874 

Lower Penobscot Veazie to Verona Island Kenduskeag 2 to 4 2,003 22,020 






Lower Penobscot Veazie to Verona Island Kenduskeag 14 to 16 83 786 




Lower Penobscot Veazie to Verona Island Kenduskeag 28 to 30 167 1,145


PRFP Page 160 

Width 


Large Parr 

Production 



Lower Penobscot Veazie to Verona Island Kenduskeag 34 to 36 1,432 7,685 

Kenduskeag Total 6,805 60,902 

Lower Penobscot Veazie to Verona Island Long Pond 0 to 2 98 1,077 



Lower Penobscot Veazie to Verona Island Long Pond 6 to 8 58 625 



Long Pond Total 836 9,070 

Lower Penobscot Veazie to Verona Island Marsh 0 to 2 98 1,077 

Lower Penobscot Veazie to Verona Island Marsh 2 to 4 1,380 15,167 

Lower Penobscot Veazie to Verona Island Marsh 4 to 6 1,017 11,085 










Marsh Total 6,018 57,904 

Lower Penobscot Veazie to Verona Island Penobscot Below Veazie 0 to 2 37 413 

Lower Penobscot Veazie to Verona Island Penobscot Below Veazie 2 to 4 751 8,253 



Lower Penobscot Veazie to Verona Island Penobscot Below Veazie 10 to 12 12 118 


Penobscot Below Veazie Total 1,859 19,404 

Lower Penobscot Veazie to Verona Island Sedgeunkedunk Stream 2 to 4 101 1,113 

Lower Penobscot Veazie to Verona Island Sedgeunkedunk Stream 4 to 6 21 234


PRFP Page 161 

Width 


Large Parr 

Production 

Lower Penobscot Veazie to Verona Island Sedgeunkedunk Stream 8 to 10 10 108 

Lower Penobscot Veazie to Verona Island Sedgeunkedunk Stream 10 to 12 210 2,143 

Sedgeunkedunk Stream Total 343 3,598 

Lower Penobscot Veazie to Verona Island Silver Lake 0 to 2 24 269 

Lower Penobscot Veazie to Verona Island Silver Lake 2 to 4 187 2,059 



Lower Penobscot Veazie to Verona Island Silver Lake 8 to 10 26 273 

Silver Lake Total 536 5,832 

Lower Penobscot Veazie to Verona Island Souadabscook 0 to 2 14 148 

Lower Penobscot Veazie to Verona Island Souadabscook 2 to 4 1,193 13,099 

Lower Penobscot Veazie to Verona Island Souadabscook 4 to 6 773 8,393 






Lower Penobscot Veazie to Verona Island Souadabscook 30 to 32 39 245 


Lower Penobscot Veazie to Verona Island Souadabscook 34 to 36 1,417 7,280 

Souadabscook Total 5,571 49,541 

Lower Penobscot Veazie to Verona Island Toddy Pond 0 to 2 59 651 

Lower Penobscot Veazie to Verona Island Toddy Pond 2 to 4 152 1,677 

Lower Penobscot Veazie to Verona Island Toddy Pond 4 to 6 103 1,121 

Lower Penobscot Veazie to Verona Island Toddy Pond 12 to 14 3 26 

Toddy Pond Total 317 3,475 

Veazie to Verona Island Total 23,617 223,939 

Lower Penobscot Total 61,932 453,271 

Grand Total 234,924 1,810,993

Appendix D - Adaptive Management Guidance for Fisheries Management in 

the Penobscot Basin 

Authors: Greg Mackey and Joan Trial 

Adaptive management is a strategy that employs the scientific method to continually 

assess and refine management. Adaptive management relies on establishing 

management plans based on a priori hypotheses (predicted results), assessment 

plans to collect data necessary to evaluate a management strategy, and a feedback 

mechanism to inform and improve management as results are obtained. Adaptive 

management is central to Atlantic salmon recovery and should be employed with all 

fish management activities in the Penobscot basin. The limiting steps in 

successfully using adaptive management are collecting sufficient data, analyzing 

and interpreting results, and using the results to improve management on a regular 

basis. Knowledge of these limitations should help managers prepare strategies to 

successfully employ adaptive management, and also to explicitly identify 

management actions where adaptive management will not be successfully used 

because of operational or budgetary constraints. 

Managers will need to create adaptive management programs for each management 

action. Although adaptive management follows well defined steps, the particulars of 

the process are project dependent and generally cannot be elucidated beforehand. 

However, some fishery management actions, such as stocking, can be generalized 

to an adaptive management approach, and this general approach can then easily be 

altered to suit needs (Table 1). 

The general adaptive management process focuses on defining goals and 

assumptions, and stating management strategy, expected outcome(s), and how 

assessment will be performed. This forces managers to clearly identify these 

elements before work is begun. This approach is easily transferrable to stocking 

(Table 2), or other management actions. 

Table 1. A general adaptive management approach adapted from S. Crawford, S. 

Matchett, and K. Reid, 2005. “Decision Analysis/Adaptive Management (DAAM) for Great 

PRFP Page 162

lakes fisheries: a general review and proposal.” 2005. Draft Discussion paper at IAGLR (International 

Association for Great Lakes Research), University of Michigan, Ann Arbor, Michigan, USA. 

1. Define the 

problem 

2. Identify 

manageme 

a. Identify core values related management objectives, including risk 

aversion levels 

b. Identify fundamental management objectives (ecological, learning, 

social) 

c. Identify key indicators or performance criteria 

d. Identify key uncertainties (uncertain states of nature) 

e. Develop qualitative or quantitative hypotheses for key uncertainties 

f. Assign prior probabilities for hypotheses 

a. Identify management alternatives 

b. Predict (calculate) the outcomes for the alternatives 

nt options 

3. Select a. Select an alternative or select competing hypotheses explaining a key 

manageme uncertainty 

nt option b. State the “value of learning” expectation for this alternative 

4. Design 

manageme 

nt plan 

5. Design 

monitoring 

plan 

6. Implement 

manageme 

a. Design implementation plan for selected alternative Or to test 

competing hypotheses 

a. Specify logistics, effort, and documentation for monitoring plan 

b. State the accuracy, precision, and power analyses 

c. Establish data management (data standards, training, QA/QC) 

d. Design data analyses (graphs, tables, statistical) 

a. Follow the implementation plan for chosen alternative 

b. Report implementation deviations 

nt plan 

7. Monitor a. Follow monitoring plan 

manageme b. Document and report deviations from monitoring plan 

nt plan c. Report if monitoring plan objective was achieved 

8. Evaluate 

results 

9. Refine the 

problem 

a. Compare predicted verses observed results 

b. Report significance of difference 

c. Assign updated (posterior) probabilities to hypotheses 

d. Report how uncertainty has been reduced (what has been learned). 

a. Re-Identify fundamental management objectives (ecological, learning, 

social) 

b. Re-Identify key indicators or performance criteria 

c. Re-Identify key uncertainties (uncertain states of nature) 

d. Re-Develop qualitative or quantitative hypotheses for key 

uncertainties in stocking 

e. Re-Assign prior probabilities for hypotheses 

10. Iterate a. Return to #2 and repeat process 

PRFP Page 163

Table 2. A generalized adaptive management approach to stocking wild captured or 

hatchery fish. 

1. Define goal(s) a. Identify goal(s) for this stocking effort 

2. Identify life history 

stage, density etc. 

3. Design stocking 

plan 

4. Design monitoring 

plan 

a. Identify the stocking alternative (life history stage, 

density, specialized rearing etc.) that is believed will be the 

most effective in achieving the goal(s) 

b. Predict (calculate) outcomes for each alternative 

c. State assumptions (identify sources of uncertainty) for 

these calculations 

d. Choose the desired stocking alternative 

e. State the value of learning for this choice 

a. Calculate the number of fish required to achieve desired 

densities. 

b. Identify when, where, and how the fish will be stocked 

a. Specify how monitoring is to be done 

b. Specify expected ability to detect success or failure 

c. Establish data management procedures 

d. Design data analyses 

a. Stock fish according to plan. 

5. Implement 

stocking plan b. Document deviations from plan 

6. Implement 

a. Follow monitoring plan 

monitoring plan b. Document deviations from plan 

7. Evaluate results a. Follow data analyses design to compare predicted 

verses observed results. 

b. Report how uncertainty has been reduced 

8. Refine stocking a. Return to #2 and reevaluate. Alter one variable in the 

approach 

stocking plan (return to #2 and repeat process). 

9. Iterate Repeat this process until stocking goal has been achieved 

An adaptive management process forces managers to state the goal (hypothesis) of 

the action and to predict possible outcomes. Stating outcomes then allows 

managers to design adjustments to the action in advance based on potential 

outcomes. This exercise is useful for three reasons: 1) it provides an objective 

statement of future management adjustments, 2) it helps define the complexity of the 

management issue- some outcomes may be so complicated that the adaptive 

management plan should be re-evaluated, and 3) it allows realistic evaluation of 

management options in advance of beginning work. 

Potential adaptive management frameworks for fry, smolt, and adult stocking 

Fry Adaptive Management 

For illustration, assume the goal of Atlantic salmon fry stocking is a given density of 

two age classes of juveniles with preferred average sizes (i.e. parr = density: 10- 

12/unit and mean fork length of 115 mm at age 1+; YOY = density 15-30/unit fork 

length 90 mm). There are 15 possible outcomes of fry stocking a reach stated 

(Table 3). Some of the outcomes feedback directly to the stocking actions with 

PRFP Page 164

ecommended adjustments. While other outcomes specify alternative strategies 

such as stocking another life stage, evaluating habitat, or re-assessing initial goals. 

More specific adjustments are possible, such as specifying an algorithm to adjust fry 

stocking numbers based on density and size of parr. 

Table 3. Draft reach specific adaptive management system for stocking juvenile 

Atlantic salmon produced at CBNFH. 

Large Pa rr YOY Actions 

Abundance Size 

D istribution 

Abundance Size 

Distribution 

Fry 

Stocking 

rate 

Obs < OK and Obs < then Increase 


options 

Obs < Sm all and Obs < Sm all then Con sider Parr Evalu ate 

habitat 

Obs < Sm all and Obs < OK or Large then Increa se Fry Evalu ate 

habitat 

Obs < La rge and Obs < then Increase 

Obs =or > OK and Obs < then N o change 

Obs =or > Sm all and Obs < Sm all then Con sider Parr Evalu ate 

habitat 

Obs =or > Sm all and Obs < OK or Large then Increa se Fry Evalu ate 

habitat 

Obs =or > La rge and Obs < then Increase Evalu ate 

Goals 

Obs =or > OK and Obs =or > then N o change 

Obs =or > Sm all and Obs =or > then R educe 

Obs =or > La rge and Obs =or > then Increase Evalu ate 

Goals 

Obs < OK and Obs =or > then Increase 

Obs < Sm all and Obs =or > Sm all then Decrease Fry Evalu ate 

habitat 

Obs < Sm all and Obs =or > OK or Large then Increa se Fry Evalu ate 

habitat 

Obs < La rge and Obs =or > then Increase Evalu ate 

Goals 

Smolt Adaptive Management 

The measureable goals of the smolt stocking program are: 

1. Maximize smolt to adult return rates 

2. Imprint smolts to reaches with spawning and rearing habitat 

3. Maximize lifetime fitness (reproductive success in wild) 

PRFP Page 165 

Other

Table 4. Data sources, parameters, data links, and adaptive management actions 

based on assessments 

Databas 

e Source 


AdultTrap 

SmoltTra 

p 

AdultTrap 

Redd 

Informat 

ion 

Numbers 

,Location 

, Marks 

Number, 

FW and 

Sea Age, 

Origin, 

Mark 

Number, 

Origin, 

FW Age, 

Mark 

In river - 

In year 

(Weldon 

and 

Veazie) 

Distributi 

on of 

Hatchery 

Cohort Calculations 

yr = Cohort 

year 

1SW = yr-1 

cohort 2SW = 

yr-2 cohort 

S1 = yr cohort 

H1W1 = yr- 

1cohort 

1SW = yr-1 

cohort 2SW = 

yr-2 cohort 

Sea age and 

mark specific 

return rates 

FW age and 

mark 

proportional 

Links to 

stocking 

Location, 

River 

Conditions, 

Timing 

Location, 

River 

Conditions, 

Timing 

Escapement, 

mark & sea 

age specific 

recapture rates Location 

redds NA Location 

Adaptive 

Management Action 

Change location if 

return rates lower than 

other sites over range 

of river conditions 

Change location if 

captures 

disproportionate to 

stocking proportions 

over range of river 

conditions 

Change location if fish 

released to river are 

not immigrating into 

spawning habitat 

Change location if fish 

released to river are 

not immigrating into 

spawning habitat 

Table 5. Adaptive management actions based on location-specific assessment of 

smolt stocking. 

Stocking Location has ____ than other stocking locations 

Smolt 

captures 

Return 

rates 

In-Year In- 

River 

Recapture 

Rates at VZ Assessment Options 

Broodstock, change 

location 

> or = > > Imprinted to lower river 

> or = > = Effective escapement Check for spawning 

> or = > < Effective escapement Check for spawning 

Imprinted to lower Broodstock, change 

> or = = > River 

location 

> or = = = Effective escapement Check for spawning 

> or = = < Effective escapement Check for spawning 

Evaluate Water Quality, 

Differential ocean smolt physiology, scale 

> or = < > survival 

loss at site 



> or = < = survival 

loss at site 



> or = < < survival 

loss at site 

Evaluate Habitat, Passage, 

Differential river Water Quality, scale loss at 

< < < or = or > survival 

site 

PRFP Page 166

Major flexibility constraints of the smolt stocking cycle (Figure 1) are hatchery rearing 

requirements and smolt transportation. Changes to some aspect of smolt rearing 

may need to be vetted a year or more in advance. Other aspects of smolt 

April 


USFWS 

Field 


Trip Plan & 

Hatchery 

Coordination 

Revise Stocking 

Plan 

USFWS 

Hatchery 

June 

Smolt Trap 


Log 


Plan 

Available 

Smolts 

SmoltTrap 

Revise Marking Plan 

January 

AdultTrap 

stocking, such as shifting a stocking location can usually be done with short notice. 

However, under adaptive management, all substantive decisions should be planned, 

following the process outline in the adaptive management section of this plan. 

Marking is the primary means of assessing management changes. Smolts marks are 

coordinated by an interagency Marking Group. All marking needs must be vetted 

through this group to ensure unique and compatible marking. 

Figure 1. Atlantic salmon smolt stocking cycle. 

Adaptive Management Adult Stocking or Transport 

November 

1. There are many potential variables that can influence the success of naturally 

spawning adults. Further, fish that have been reared and released under 

artificial circumstances carry another set of factors that will affect the 

outcome. 

2. Projects should attempt to control for some extraneous factors. 

PRFP Page 167 

July 

Adult Trap 

Cohort Age, Origin, 

& Mark Analyses 

Review 

Previous 

Years 

Stocking & 

Marking Plans 

December 

Place 

Hatchery 

Order 

October

3. Results (hypotheses) with linked management options should be stated a 

priori, and assessments should be designed to address these. 

4. Adaptive management should occur at the project and program scales. That 

is, how successful was the project, and how does this level of success fit in 

with the overall program? 

5. Assessment of results and subsequent management actions should 

emphasize potential to restore naturally reproducing populations. 

Table 6. Adaptive management actions related to actions that increase adult 

escapement, based on expected YOY and parr abundances and size 

distributions and two redds/female. 

YOY Parr 

Result Abundance Size Abundance Size Action 

Low redd to 

female ratio 

< = < = 

Assess adult rearing methods. 

Assess origin of fish. Increase 

stocking numbers 


female ratio 

= = = = 

Assess field methods 

No project changes 


female ratio 

> = > = 




female ratio 

> < > < 


Density dependence? Reduce 


OK redd to 

female ratio 

< = < = 


Assess origin of fish. 


female ratio 

= = = = No project changes 


female ratio 

> = > = 




female ratio 

> < > < 




High redd to 

female ratio 

< = < = 




female ratio 

= = = = No project changes 


female ratio 

> = > = No project changes 


female ratio 

> < > < 




PRFP Page 168

Table 6. Continued. 

YOY Parr 

Result Abundance Size Abundance Size Action 


Low spatial 

dispersal 

< = < = 

Assess origin of fish. Consider 

more stocking locations. 

Change stocking timing. 


Low spatial 

dispersal 

= = = = 





Low spatial 

dispersal 

> = > = 





Low spatial 

dispersal 

> < > < 




Expected 

dispersal 

< = < = 



Expected 

dispersal 

= = = = No Change 

Expected 

dispersal 

> = > = No Change 

Expected 

dispersal 

> < > < 




High spatial 

dispersal 

< = < = 

Assess origin of fish. Change 

stocking timing. Revise 

expectations 


High spatial 

dispersal 

= = = = 

Assess origin of fish. Change 

stocking timing. Revise 

expectations 

High spatial 

dispersal 

> = > = 


Assess origin of fish. Revise 

expectations 

PRFP Page 169

Given juvenile abundances at the YOY or parr stages, do progeny of naturally 

spawning adults fail to meet, or exceed other stocking strategies? Can adjustments 

be made to enhance this, or does there appear to be no advantage? Do these fish 

return at a higher rate as adults? Do these fish have a higher lifetime reproductive 

success? 

Projects should detail hypotheses (alternative outcomes) based on the design of the 

project. Ideally, a table of adaptive management outcomes and actions can be 

created for each project. Furthermore, assessment personnel should draw on 

adaptive management scenarios from other sources in this document, as suitable. 

For example, the fry stocking adaptive management outcomes may be suitable for 

later life stages under the adult escapement section. 

PRFP Page 170

Appendix E - Atlantic Salmon Fisheries Management Options and Strategies 

Author: Oliver Cox 

This section lays out the fisheries management options for Atlantic salmon and 

presents an overarching structure in which to implement these strategies. There are 

eight major categories of fisheries enhancement that we use with Atlantic salmon: 

1. Egg planting or streamside incubation 

2. Fry stocking 

3. Parr stocking (fall parr, 0+ from GLNFH or CBNFH) 

4. Smolt stocking 

5. Trap and truck sea-run adults 

6. Artificially reared adult stocking 

7. Rejuvenated kelt adult stocking 

8. Natural reproduction- no stocking 

Most of these are used at some level, or have been in the past. Some of these 

methods are standard management practice, such as fry and smolt stocking, while 

others are experimental such as egg planting and adult stocking. However, under 

an adaptive management framework, all management methods should be evaluated 

using the scientific method. The major difference between management options is 

scale and assessment intensity. 

At this point, we do not fully understand the potential of any of these methods to 

recover Atlantic salmon populations. We do understand the potential of many of 

these methods within certain bounds, but not to the level of lifetime fitness and 

population recovery. Therefore, all methods should be considered and tested 

against one another. Management decisions about methods on which to focus 

should rely on existing program specific data specific and the scientific literature. At 

the moment, egg planting, rejuvenating kelts for stocking and stocking artificially 

reared adults are not used in the Penobscot basin. Adult stocking is being used in 

the Sheepscot River, Sandy River, Machias watershed, East Machias watershed, 

and Hobart Steam. Intensive work on streamside incubation and egg planting is 

also underway in the Sandy and Sheepscot. However, this work has not tested searun 

eggs. Such eggs are available in the Penobscot, and this present an opportunity 

to add important information about egg source/quality to the work already underway. 

Structure of Atlantic Salmon Fisheries Management Actions 

Fisheries management takes place in two dimensions: space and time. We initially 

consider space, then time: 

1. Use management actions in discrete areas of the Penobscot basin. This will 

enhance assessment and provide a more explicit result if a strategy proves 

successful. Keeping management actions separated in space can also 

maintain independence among actions. Areas of the basin should be 

PRFP Page 171

identified a priori for all potential management actions, regardless if they are 

currently being used. Create a GIS layer to store and display this structure. 

2. Consider temporal isolation or spacing of management actions and use to 

achieve a structure that will provide clear assessment opportunity and avoid 

confounding factors. 

3. Establish specific strategies within a management action. For example, fry 

may be stocked at certain densities, DIs, by point stocking, or stratified by 

stream/habitat characteristics. Each strategy will have testable hypotheses. 

This is the time to make adjustments, ranging from small changes to 

completely new ideas. 

4. Establish assessment plans for each management strategy. Clearly state the 

measure(s) that will be used to test efficacy. 

Egg Planting and Streamside Incubation 

Eggs may be planted in a variety of ways at either the green or eyed stage. Green 

egg planting would occur in the fall during spawning time. Eyed egg planting would 

occur in the winter, typically January or February. Eggs may be planted in 

naturalistic artificial redds, in a variety of instream incubation units, or in streamside 

rearing units. The efficacy of these approaches is being evaluated elsewhere at this 

time. 

Egg planting affords a nearly complete natural rearing history for the juvenile fish, 

with the streamside tanks likely having the largest domestication influence. The fish 

incubate under ambient stream water conditions, should emerge in synchrony with 

their wild counterparts, and enter the stream environment in essentially the same 

manner as wild fish. 

Egg planting provides one of the two most naturalistic approaches for introducing 

juvenile fish (along with adult stocking) to the environment. It also affords managers 

the ability to target areas to introduce specific numbers of eggs to be introduced. 

However, egg to fry survival is more variable than in the hatchery, and planting eggs 

is labor intensive. Egg planting is probably most appropriate for streams with quality 

juvenile rearing habitat. It may be less effective in areas where rearing habitat is 

less appropriate for fry. Planting eggs also is contingent on stream conditions, high 

water and ice cover. 

Fry Stocking 

The existing fry stocking practices are based on previous work by MASC, PIN, and 

southern New England Atlantic salmon program biologists. The objectives are to 1) 

populate high quality habitat that would most likely not be populated through 

spawning escapement to maximize smolt production; 2) buffer habitat where Atlantic 

salmon spawned naturally; 3) optimize the stocking of river reaches that can 

PRFP Page 172

easonably be accessed; and 4) minimize fishery management conflicts with 

MDIFW. Fry may be stocked in either a fed or unfed state. Unfed fry offer the 

advantages of not requiring financial and staff resources for feeding, and limit 

hatchery discharge. Fed fry are stocked already feeding, assuring managers that 

the fish have made the transition to exogenous feeding. Fry are stocked in May and 

June. The optimal water temperatures, time of year, flows, and other environmental 

variables that influence the success of fry stocking are not well understood. 

Fry represent the life stage of free-swimming fish that have the least domesticating 

selection pressure. Fry live virtually their entire free-swimming lives under natural 

conditions, and so survivors should theoretically have greater fitness than fish 

stocked at later juvenile stages. Managers can target specific fry densities for 

specific reaches of stream. Managers can also choose to carefully distribute the fish 

at even densities, or to stock them in larger groups (point stocking), and allow the 

fish to disperse. Point stocking reduces handling of the fish and may offer some 

advantage in predator swamping and natural recruitment to areas of the stream, 

while more incremental stocking offers the advantage of placing fish in appropriate 

habitat at desired densities. 

Fry suffer high mortality once they enter the river, although the sources of this 

mortality are not clear. Nevertheless, they undergo a strong period of natural 

selection. Although fry stocking can introduce large numbers of fish, it does not 

necessarily translate into robust parr and smolt populations. Fry stocking is most 

appropriate for streams with quality juvenile rearing habitat. It may be less effective 

in areas where habitat is less appropriate for fry. 

Parr Stocking 

The current parr program on the Penobscot is a result of Green Lake National Fish 

Hatchery needing to reduce salmon densities as fish become crowded in the pools. 

Parr (0+) have been stocked in lieu of fry stocking in an effort to circumvent high 

rates of early mortality suffered by fry. Parr stocking may also be effective in areas 

where fry stocking is less effective, either due to mortality or emigration. Parr are 

reared for a longer time than fry in the hatchery, and thus are prone to greater risk of 

domesticating selection and negative effects of hatchery rearing on behavior. The 

optimal time to stock parr is unclear; however, stocking has typically occurred in 

September when water conditions have cooled somewhat, but there is still time for 

the fish to acclimate before winter. Stocking rates should target desired parr 

population densities, adjusted for post-stocking survival and interactions with 

resident fish. Parr stocking require greater hatchery resources and creates greater 

hatchery discharge. It also may limit hatchery rearing space for other life history 

stages. 

Parr stocking is likely to be more prone to negative interactions with resident fish. 

While fry can be stocked to avoid areas of natural reproduction, resident parr are 

PRFP Page 173

distributed throughout the river and stocked parr will likely be introduced in areas 

with resident fish. Therefore, managers must question if they are achieving a net 

gain of fish without the loss of the more desirable resident fish. Furthermore, the 

need to stock parr may be indicative of a habitat problem that limits the use of fry. If 

this is the case, then restoration via parr stocking is likely to fail because the habitat 

cannot support all life history stages of salmon. 

Parr stocking is most appropriate for reaches of stream that are not well suited for 

fry. In addition, parr stocking may prove to be an effective approach in place of fry 

stocking. At this point, the efficacy of parr stocking is unclear, as are the risks to the 

resident population. 

Smolt Stocking 

Smolt stocking circumvents pre-migratory natural mortality, and is the most likely 

stocking method to produce the most adult returns. However, smolt stocking has 

several detractions. It requires substantial rearing space, produces more discharge, 

and requires more resources at hatcheries. 

Hatchery smolts do not survive as well at sea as wild fish, and therefore smolt 

stocked fish must overcome this lower survival with greater numbers. Many factors 

may affect the survival of hatchery smolts: size, growth rate, physiological readiness, 

coloration, and behavior. Hatchery smolts have not reared in their “natal” stream, 

and have been shown to have higher rates of straying than wild fish. They also may 

not be as effective homing to quality spawning areas within their natal stream. They 

lack rearing experience under natural conditions, and this may interfere with their 

ability to reproduce. Smolt stocking avoids the resident fish interaction issues faced 

with parr stocking. Some research has shown that adults derived from hatchery 

smolts tend to have lower reproductive success than their wild counterparts. If this 

is true in our program, then hatchery smolts would need to overcome both lower 

ocean survival and lower reproductive success by returning more fish on a per 

capita basis to achieve a given level of natural reproduction by adult escapement to 

the rivers. 

Smolt stocking is most appropriate when returning adults is paramount. However, 

managers need to consider the tradeoff between adults derived from hatchery 

smolts verses naturally reared smolts. Smolt stocking tends to be an immediate way 

to increase adult returns, but is arguably not an effective way to restore a population, 

as evidenced by the vast numbers of smolts of various salmon species stocked and 

the continuing decline in the populations they are intended to support. The numbers 

of smolts to stock should be calculated based on the desired number of adult 

returns, but is often limited by rearing space. When other methods of stocking fail, 

particularly fry stocking, managers often turn to smolt stocking. However, this failure 

is likely the result of habitat deficiencies that limit survival through a complete life 

history cycle. Therefore, smolt stocking may merely bypass a habitat problem, but if 

this is the case, will not be effective in recovering the population. 

PRFP Page 174

Approximately 600,000 smolts are stocked in the Penobscot basin annually, 

accounting for 90% or more of the adult Atlantic returns. Major factors that affect 

where and when to stock smolts are: 1) homing to suitable habitat, 2) survival due to 

migration through dams, 3) seasonal timing, and, 4) physiological timing. Additional 

consideration should be given to smolt “quality”. Alternative rearing and release 

strategies may improve survival. 

Currently, smolts are stocked at a number of fixed locations. These have been 

adjusted over time, with the most recent adjustments based on relative return rates 

among stocking locations. The adaptive management decision based on these 

findings was to shift smolts from the lowest return rate location to a higher return rate 

location. 

Major constraints on system flexibility are hatchery rearing requirements and smolt 

transportation. Changes to some aspect of smolt rearing may need to be vetted a 

year or more in advance. Other aspects of smolt stocking, such as shifting a 

stocking location can usually be done with short notice. However, under adaptive 

management, all substantive decisions should be planned, following the process 

outline in the adaptive management section of this plan. Marking is the primary 

means of assessing management changes. Smolts marks are coordinated by an 

interagency Marking Group. All marking needs must be vetted through this group to 

ensure unique and compatible marking. 

Up until 2006, there was no single reference stocking location that could be used to 

track temporal changes in return rates. Whole cohort return rates are the only long 

term data, and offer not options to compare alternative stocking strategies. In 2006, 

the decision was made by TAC to establish a long-term baseline return rate site. 

From 2006 to present, 175,000 marked smolts have been stocked at Morin Fuel in 

Bradley. This was the location selected to use as the baseline location prior to any 

dam removals. The smolts stocked in Bradley have carried three different VIE 

marks and were stocked on several dates with equal numbers of all three marks. 

This marking strategy provides an estimate of return rate for each cohort with a 

variance. The baseline site will change to a location above Milford in anticipation of 

the Milford fish lift coming online and Veazie being removed. This plan results in a 

long-term baseline return rate site above Milford. 

The stocking plan for 2007 and 2008 was: 

~ 175,000 tagged PN stocked in Veazie pond (Morin Fuel) 

~ 200,000 PN stocked in the Pleasant River (Milo) 

~ 200,000 PN stocked at near West Enfield smolt ponds or Passadumkeag boat 

launch 

~ 25,000 PN stocked into West Enfield smolt ponds 

PRFP Page 175

Fish are distributed between ICES Standard Weeks 15 and 19 (9 April to May 13) 

ensuring that each location is stocked throughout the time period (not all the smolts 

at any one location are stocked on one date). 

This plan will continue through 2009, but should be reviewed and revised based on 

redd distributions, returns to Weldon, and other data on distribution of adults 

throughout the drainage. 

Adult Stocking or Transport 

Stocking sexually mature adults bridges the gap between the most highly 

domesticated life history stage stocked (adult) and the most natural life history stage 

introduced into the stream (naturally spawned eggs). Domestically reared adults 

undergo the most extensive domestication selection of all life history stages. 

Therefore, they typically perform poorly in natural reproduction compared to wild 

adults. However, despite this shortcoming, they may be a valuable tool in 

restoration because they offer one of the most naturalistic pathways to populate the 

rivers with juvenile salmon. In particular, stocked adult fish must undergo the same 

natural and sexual selection regimes that wild fish do once in the river at spawning 

time. This is absent in other stocking strategies. Their progeny are the result of 

natural spawning where reproductive behavior, nest site selection, mate selection, 

spawning time, and nest construction have all survived the test of natural and sexual 

selection. Potential drawbacks of adult stocking include: 1) managers often have 

limited control over where the fish spawn, 2) spawning timing is often asynchronous 

with natural conditions (late spawning), 3) stocked fish may introduce excessive 

competition with wild fish for spawning locations or mates, 4) stocked fish may 

superimpose redds on wild redds, 5) rearing adult fish requires substantial hatchery 

spaces and resources and may increase hatchery discharge. 

The effectiveness of adult stocking is still in question. Recent attempts to stock 

adults in Maine have generally shown poor results, but with more recent positive 

results. Assessment is still underway, but CBNFH reared adults seem to be able to 

produce juvenile densities similar to fry stocking, and their progeny may have higher 

fitness than fry stocked fish. Adult stocking may be used to bypass high mortality at 

any life history stage (particularly smolt to adult), but alternatively, it is perhaps the 

method that requires habitat be considered most carefully because the entire life 

history of the salmon is represented with this approach. The early life history 

experience of stocked adults may be important in the reproductive success, as are 

rearing the fish to naturalistic size, and stocking them at advantageous times of year. 

The best time to stock adult fish is unclear, but arguments can be made to introduce 

them as early in the fall as possible, or in spring/early summer. 

The current restoration program routinely produces adult fish that are excess to 

hatchery needs. However, the need for these fish in the hatchery is often not 

established until early fall. Thus, stocking time may be constrained by hatchery 

PRFP Page 176

operations. Adult fish reared specifically for adult stocking should be stocked at a 

time of year thought optimal for their success. This will likely need to be tested 

because we do not know the best time of year to stock these fish. Furthermore, 

adult fish intended to be stocked in the rivers, whether reared solely for that purpose 

or as a byproduct of other restoration approaches, should be reared to optimize 

natural reproductive success. Therefore, they should be within the natural size 

range of the fish, be physiologically in synchrony with the natural environment, and 

reared under conditions that allow juveniles to establish territories. Adult fish may 

move substantial distances and managers must either restrict their movements or be 

prepared for the fish to leave the reaches where they were stocked and reproduce 

elsewhere. 

PRFP Page 177

Appendix F - Atlantic Salmon Strategic Objectives 

Goals and Objectives for Atlantic Salmon Restoration in the Penobscot River 

Basin 


Introduction 

Goals and measurable objectives will be critical in translating policy into action and 

applying science to the recovery of Atlantic salmon in the Penobscot basin. Setting 

measureable, quantifiable objectives presents a difficult challenge for managers due 

to the uncertainty inherent in ecological systems, but offers the ability to design 

programs and actions to meet goals, and to continually assess progress towards 

those goals (Tear et al. 2005). Here we present the overarching goal for salmon in 

the Penobscot and a set of measureable objectives. Also included are the 

measures that will be used to assess progress towards meeting an objective, as well 

as some of the potential strategies. Several sources of uncertainty exist that are 

beyond the control of biologists, and therefore could affect outcomes despite best 

efforts. Notably, marine survival is a major driver of Atlantic salmon populations and 

it is unlikely that humans can affect this in the short-term. Numerous dams exist in 

the basin affect both up and downstream passage. Although these are under 

human control, forces beyond biological management will influence decisions 

regarding dams that affect fish passage. The freshwater habitat has been greatly 

altered since European contact. The extent to which the freshwater habitat may 

need improvement is unclear, but should extensive habitat improvements be 

required, financial and logistical constraints may hamper restoration. Finally, how 

climate change will affect the system is unknown. 

Strategies and actions within those strategies will be developed for the operational 

plan and implemented under these objectives. Hereafter, adaptive management of 

the Penobscot will focus on actions and assessments that move the restoration 

process closer to the objectives, and therefore the goal. Strategies or actions that 

do not show relevance to or progress towards an objective should be adjusted or 

eliminated in favor other approaches. Strategies or actions that do show success 

should be used more widely. Proper assessment will be vital to the success of this 

objective-driven approach. We will develop a series of annual assessments to track 

overall progress. Further, on an annual basis lead scientists will meet to perform 

analyses, interpret results, and make recommendation for future management. 

PRFP Page 178

Methods 

We chose to divide the Penobscot into seven sub-drainages based on salmon 

homing theory and drainage geography (Figure 1). The Lower and Mid-Penobscot 

areas do not constitute discrete sub-drainages like the other areas, and therefore 

how the population structure would functions is not as clear as in the more discrete 

areas. However, they offer for management and strategic efficiencies. The 

Penobscot system will be managed assuming that differentiated populations will 

eventually arise as restoration progresses. 

Figure 1. Recovery Sub-Drainages of the Penobscot Basin: 

1. Lower Penobscot 

2. Piscataquis 

3. Pleasant 

4. East Branch 

5. Mattawamkeag 

6. Passadumkeag 

7. Mid-Penobscot 

PRFP Page 179

We made some key assumptions about salmon restoration: 

1) The Penobscot basin contains seven discrete areas where unique 

populations should exist (West Branch is not included) 

2) Each area could support a self-sustaining population 

3) “Wild” means fish of completely natural heritage: the progeny of sea-run 

parents (adult stocked progeny, egg planting and fry stocking are NOT 

included in this group) 

4) Restoration resources will remain constant and can be shifted and 

concentrated in target sub-drainages as other sub-drainages are restored. 

We developed quantitative criteria in part by applying well recognized standards (e.g 

effective population size of 500), using data analysis from local research (quantile 

regression model linking juvenile densities to stream size), and used best 

professional judgment and tried to make the measures logical when taken together. 

Goals and Objectives 

Goal: Sub-Goal for Atlantic Salmon: Rebuild Atlantic salmon populations to 

stable, self-sustaining status with recreational fishable surplus. 

Objective 1: Meta-population capable of self-sustaining status and providing a 

recreational fishable surplus for 100 years with 95 % certainty. 

• Measure 1a: Within each sub-drainage: Ne > 500 exceeded by 20%, or 

sub-drainage-specific CSE exceeded by 20% on annual basis. [Use 

multiple (3) models to predict necessary population levels. Arrive at 

consensus among models.] Use the measure that is lowest for each 

sub-drainage. 

o Estimate Ne using modeling or algorithm based on N. 

o Estimate Ne using genetic assessment 

o Redd counts extrapolated to # spawners 

o Trap Counts 

o Telemetry Estimates 

� Strategy- meeting objectives listed below will lead to this 

objective. Develop plan for success: How and when to 

stop stocking as populations recover. Use modeling and 

habitat estimates to create sub-drainages size targets 

with uncertainty included. 

� Strategy- manage populations to achieve CSE objective 

by considering all populations and targeting those most 

likely to recover first. Use adaptive approach to improve 

management for later populations. 

� Strategy- Shift resources to new sub-drainages as others 

are restored. 

PRFP Page 180

• Measure 1b: Sub-drainages with growth rate R equal to or greater 

than 1. 

o Estimate from adult to adult cohort returns (trap census or redd 

counts) 

o Estimate using modeling (PVA or matrix etc.) based on other 

available life stage data. 

� Strategy- focus management activities and assessments 

on population growth rates. Sub-drainages where natural 

reproduction is inadequate will never recover. 

Management must focus on growth rates as well as 

population size. 

� Develop assessment plan that will allow detection of subdrainage 

growth rates (e.g. concentrated redd counts, 

proportional adult returns estimated by telemetry etc.) 

Table 1. Year and Percentage of Criteria Met for Sub-drainages 1-7 

Sub-Drainage 

Year 1 2 3 4 5 6 7 

0 0 % 0 % 0 % 0 % 0 % 0 % 0 % 

5 20 % all 0 % 0 % 0 % 0 % 0 % 0 % 

10 20 % wild 20 % all 0 % 0 % 0 % 0 % 0 % 

15 50 % wild 20 % wild 20 % all 20 % all 0 % 0 % 0 % 

20 90 % wild 50 % wild 20 % wild 20 % wild 20 % all 20 % all 20 % all 

25 restored 90 % wild 50 % wild 50 % wild 20 % wild 20 % wild 20 % wild 

30 restored restored 90 % wild 90 % wild 50 % wild 50 % wild 50 % wild 

35 restored restored restored restored 90 % wild 90 % wild 90 % wild 

40 restored restored restored restored restored restored restored 

Key to table: 

0 % No demographic measures achieved 

20 % all 20 % of demographic measures is achieved considering both wild and 

hatchery fish. 

20 % to 90 % wild 20 % to 90 % of demographic measures is achieved by wild fish only. 

restored All demographic measures achieved with a wild population (no hatchery 

supplementation). 

Figure 2. Generalized Sub-Drainage Recovery and Percentage Wild Fish Curves 

PRFP Page 181

Number of Sub-Drainages Recovered 

7 

6 

5 

4 

3 

2 

1 

0 

Number of Sub-Drainages 

Wild Percentage 

2009 2014 2019 2024 2029 2034 2039 2044 2049 

year 

Objective 2: Increase natural spawning to 100% of production by wild spawners in 

40 years 

• Increase wild proportion of overall escapement of wild sea-run and 

hatchery-derived adults, with wild fish meeting Objective 1 (Table 1). 

o Trap counts 

o Redd counts 

� Strategy- Penobscot Broodstock Management Plan will 

be developed to help address this. Think creatively as to 

how this can be accomplished. 

� Strategy- Increase freshwater production by habitat 

improvement, connectivity, intrinsic productivity, etc. 

• Increase the number of hatchery-derived adults spawning naturally to 

augment wild spawners by doubling the 2008 number in 5 years in at 

least one sub-drainage, increasing by additional 50 % in 10 years in at 

least two sub-drainages, and no augmentation in 40 years. 

o Release data 

o Redd counts 

� Strategy- Penobscot Broodstock Management Plan will 

be developed to help address this. Think creatively as to 

how this can be accomplished. Identify areas for adult 

stocking. Use adaptive management to assess results 

and aggressively adapt to information. 

PRFP Page 182 

100 

90 

80 

70 

60 

50 

40 

30 

20 

10 

0 

Percent Wild Fish

Objective 3: Discontinue supplementation in sub-drainages meeting Objective 1 

measures (Table 1). Stocking should be halted at the earliest point possible to 

encourage re-population by wild fish. By year 40, all salmon will be of wild origin. 

• Evaluate using stocking records/recommendations. 

� Strategy- Develop a plan for success- how and when to 

stop stocking. This must be peer-reviewed and should 

be a central tenet of the salmon program in Maine. 

Constantly assess populations to determine if stocking is 

warranted under this plan. 

� Develop explicit adaptive management plan to halt 

stocking based on Table 1 measures. 

Objective 4: Achieve self-sustaining smolt to adult return rates within five years of a 

sub-drainage achieving 20 % of Objective 1 measures for hatchery and wild fish 

combined (Table 1). Also assess hatchery-derived smolt to adult return rates that 

could lead to self-sustaining populations. Use trapping facilities to assess smolt to 

adult return rates. 

• Measure 4a: Estimate required return rates for self-sustaining 

population annually based on population data and PVA model. 

� Strategy- use modeling to set targets with uncertainty. Test 

models against empirical data as they become available. 

Adjust models as needed to improve target(s). 

• Measure 4b: Return rates based on marked groups at Veazie and/or 


� Strategy- stock marked smolts and set up proper sampling 

scheme to assess return rates of hatchery fish. Compare to 

wild. Adapt as necessary to improve. Change rearing 

regime/environment, stocking methods (timing etc.). 

• Measure 4c: Naturally reared return rates 

� Strategy- Estimate natural return rates via juvenile or smolt 

assessments and returning adult census (trap or redd 

counts). Use data from un-dammed rivers to augment our 

understanding. Test against rates needed for recovery. Use 

information to address habitat/environment issues. 

• Measure 4d: Smolt to adult return rates (SAR) 

o Stocked above one dam 

o SAR based on stocking location 

� Strategy- Assess smolt return rates in relation to stocking 

location and dams. Identify opportunities (promising return 

rates) and problems (return rates that are unlikely to yield 

recovery). Aggressively pursue proactive management in 

promising areas and identify limiting factors in problem 

areas. Shift resources away from problem areas until 

limiting factors have been addressed. 

• Measure 4e: Number of returns to Weldon as a proportion of what is 

stocked upstream. 

PRFP Page 183

� Strategy- Use stocking data and trap data to determine 

survival and homing of fish stocked above Weldon. Shift 

management resources away form areas that have limiting 

factors that likely prevent recovery and aggressively manage 

areas that are promising for recovery. 

• Measure 4f: Return rate and number of rejuvenated kelts 

� Strategy- Estimate kelt to spawner survival. Use data to 

improve population models. Determine if this survival can be 

improved. If so, pursue actions to improve if modeling 

suggests a worthwhile benefit of the population. 

� Strategy- Assess the potential of kelt rejuvenation. Do 

experimental work if needed. Use modeling to predict 

benefit and help make management decision as to value of 

such a program. 

Objective 5: Achieve interim juvenile life stage-specific measures to assess progress 

towards goal and to inform management at specific shorter time intervals. Achieve 

within five years of a sub-drainage achieving 20 % of Objective 1 measures for 

hatchery and wild fish combined (Table 1). Applies to both hatchery and wild fish, 

but applies to wild fish only to reach Objective 1. 

• Measure 3a: On average > = 240 eggs per unit deposition on annual 

basis within five years of a sub-drainage achieving 20 % of Objective 1 

measures for hatchery and wild fish combined (Table 1). 

o Redd counts extrapolated to # eggs 

� Strategy- Improve fish passage 

� Strategy- stock adults 

� Strategy- trap and truck sea-run adults 

� Strategy- Increase upstream escapement by decreasing 

broodstock take and/or increasing adult returns. 

� Strategy- Develop more precise egg deposition rates for 

sub-drainages. 

• Measure 3b: Use following measures (3c-3e) for hatchery and wild 

juveniles. Compare hatchery verses wild survival and/or population 

densities and smolt production. 

• Measure 3c: > = 90 % density quantile (from cumulative drainage area 

quantile regression model) or greater YOY and parr per unit of habitat 

within five years of a sub-drainage achieving 20 % of Objective 1 

measures for hatchery and wild fish combined (Table 1). Electrofishing 

estimate or CPUE equivalent 

� Strategy- Stock fry and improve fry stocking methods 

� Strategy- Stock eggs and improve egg stocking methods 

� Strategy- Stock reaches most likely to yield desired 

densities 

� Strategy- Increase connectivity 

� Strategy- Improve habitat complexity 

PRFP Page 184

� Strategy- Assess environmental conditions that are 

limiting 

� Strategy- Use quantile regression model coupled with 

development of adaptive management criteria based on 

quantiles. 

• Measure 3d: > = 3 smolts per unit (240 eggs/unit*0.0125 or estimate 

from parr quantile regression and typical smolt survival) within five 

years of a sub-drainage achieving 20 % of Objective 1 measures for 

hatchery and wild fish combined (Table 1). 

o Smolt trap or other estimation method 

� Strategy- See 3c above… 

• Measure 3e: Egg to smolt survival of > = 1.25% within five years of a 

sub-drainage achieving 20 % of Objective 1 measures for hatchery and 

wild fish combined (Table 1). 

o Analysis of data 

� Strategy- See 3c above… 

� Collect appropriate juvenile abundance data and smolt 

data to assess. Use un-biased sampling approach. 

Objective 6: Increase upstream migratory survival rate within 15 years to allow selfsustaining 

levels. 

• Measure 6a: Improve upstream fish passage at dams to levels needed 

for self-sustaining population 

� Strategy- Estimate required passage efficiencies 

� Strategy- Review current information and use to direct 

further action under this objective. 

� Strategy- Assess fish passage at all dams as needed 

within 5 years 

� Strategy- Complete improvements based on passage 

efficiency and population effect within 10 years. 

� Strategy- Target current focus restoration areas. 

• Measure 6b: Improve stream connectivity (small dams, culverts etc.) to 

levels needed to achieve desired Ne and N. 

� Strategy- Assess connectivity limitations within 5 years 

� Strategy- Fix connectivity problems based on passage 

efficiency and population effect within 10 years 


Objective 7: Increase downstream migratory survival rate within 15 years to allow 

self-sustaining levels. 

• Measure 7a: Improve downstream fish passage at dams to levels 

needed for self-sustaining population 

� Strategy- Estimate required passage efficiencies 

� Strategy- Review current information and use to direct 

further action under this objective. 

PRFP Page 185

Reference 

� Strategy- Assess fish passage at all dams as needed 

within 5 years 

� Strategy- Complete improvements based on passage 

efficiency and population effect within 10 years. 


• Measure 7b: Improve stream connectivity (small dams, culverts etc.) to 

levels needed to achieve desired Ne and N. 

� Strategy- Assess connectivity limitations within 5 years 

� Strategy- Fix connectivity problems based on passage 

efficiency and population effect within 10 years 


Tear, T. H., P. Kareiva, P. L. Angermeier, P. Comer, B. Cech, R. Kautz, L. Landon, 

D. Mehlan, K. Murphy, M. Ruckleshaus, J. M. Scott, and G. Wilhere. 2005. 

How much is enough? The recurrent problem of setting measureable 

objectives in conservation. BioScience. 55. 835-849. 

PRFP Page 186

Appendix G - Habitat Survey and Assessment Plan for the Penobscot Basin 


Currently there is substantial coverage of Atlantic salmon habitat survey in the 

Penobscot basin. However, the size of the basin precludes any type of 

comprehensive field survey of salmon habitat. Such surveys are valuable because 

they not only provide data of immediate use to managers and policy makes, but also 

provide baseline data for various modeling efforts. In addition to the field survey of 

habitat, the entire Penobscot basin, as well as all Atlantic salmon waters in the state, 

has had Atlantic salmon habitat estimated via a GIS model. Further refinement of 

this model is planned. 

Habitat Survey 

Field survey of habitat should continue to use the DMR BSRFH “Big River” habitat 

survey method and focus on waters of importance to salmon management, but also 

focus on surveying a diversity of stream types (size, gradient, geographic location). 

This will help managers understand the scope and frequency of habitat across 

various stream types. Such surveys will also help to validate modeling efforts, 

providing more and faster habitat information with estimates of precision at lower 

cost. A sampling plan for habitat survey will be established by biologists familiar with 

the basin and with the GIS habitat model. Such a survey may include stream 

reaches randomly chosen for a defined sampling frame. On an annual basis, a 

portion of each summer will be allotted to habitat survey, with balance between 

habitat assessment and survey. 

Habitat Assessment 

Large Woody Debris 

Recent surveys in coastal Maine rivers have revealed that large woody debris (LWD) 

is at extremely low levels. A study is underway to test the effectiveness of adding 

LWD to salmon habitat. However, no surveys have been done in the Penobscot 

basin, nor in more inland Maine rivers. The Penobscot basin contains a wider array 

of land use activities, forest types, and landscape features than does the coastal 

area where previous surveys were done. Therefore, performing LWD surveys 

across reaches with different stream sizes, forest stands, topography, and land use 

history would help link LWD loading to these variables. Assuming a link is revealed, 

we can use this information to predict LWSD loadings in other streams. One avenue 

that may aid in this is using an LWD loading model based on forest stand data, 

environmental variables, and stochastic events. Field surveys will help validate the 

model and allow broader inferences to be made. 

PRFP Page 187

Water Temperature 

Water temperature is recorded annually at various sites in the Penobscot, in 

cooperation with Penobscot Indian Nation, who also record water temperatures. 

Water temperature monitoring in the Penobscot basin falls within a larger state-wide 

water temperature monitoring plan for Atlantic salmon waters. Recently, DMR 

BSRFH has been scaling back the number of temperature loggers deployed 

annually, and is concentrating on monitoring key index sites and using additional 

loggers to rotate among sites for interest. This correlates water temperatures at new 

sites to the index site(s) and allows a prediction model to be constructed. Water 

temperature should continue to be recorded at index sites, while additional loggers 

shall be deployed at sites of interest. New sites may be chosen using a GTRS 

method. This will provide unbiased water temperature information for the basin. 

The amount of effort to put into water temperature monitoring should be kept at or 

below current levels, unless a well-defined study is put forth. More effort should be 

put into analysis and interpretation of water temperature data. Notably, a stream 

classification system should be finalized and put into general use statewide (Figure 

1). 

Figure 1. Stream classification system based on summer water temperature 

variability and magnitude. 

Temperature Range 

Connectivity 

Extreme 

(> 6°) 

Moderate 

(3-6°) 

Stable 

(< 3°) 

Cold/Extreme Cool/Extreme Warm/Extreme 

Cold/Moderate Cool/Moderate Warm/Moderate 

Cold/Stable Cool/Stable Warm/Stable 

Cold (< 16°) Cool (16 - 22°) Warm (> 22°) 

Average Temperature 

Fish passage at dams 

Pursue additional fish passage studies (Atlantic salmon adult and smolt, other 

species as needed) at dams where studies have not been done, are incomplete, out 

of date, or insufficient. Such information is critical for large scale management 

decisions. Without knowledge of dam-related mortality, all management actions 

PRFP Page 188

elated to diadromous fishes upstream are at risk of failure if dam-related mortality is 

too high to allow viable populations. Establish a team to pursue such studies on an 

ongoing basis. 

Stream connectivity 

Stream connectivity surveys have been underway in the Penobscot basin. These 

surveys are planned to continue. Information form these surveys will be used to 

make decisions on fixing stream connectivity problems. These actions should be 

orchestrated to 1) address stream connectivity in the areas that will most benefit 

Atlantic salmon (generally the most productive habitat), and 2) in subdrainages that 

are more likely to allow viable populations to persist. In additions, stream 

connectivity restoration should be done from downstream to upstream. Stream 

connectivity survey data can also be used to model the amount of accessible (or 

inaccessible) habitat, and, therefore, predict production potential more accurately. 

PRFP Page 189

Appendix H - Developing a Sampling Plan for the Penobscot Basin 


Introduction 

The Penobscot Basin is the largest river system in Maine and is managed for 

Atlantic salmon and other diadromous fishes in the context of a state-wide setting. 

Sampling natural systems for management requires unbiased and spatially 

distributed sampling, with samples spaced relatively evenly in space. Sampling 

must balance trend and status data collection goals. In addition, sampling should 

allow for greater emphasis (sampling) effort within certain areas depending on needs 

of biologists and managers. Finally, sampling must be flexible to allow un-sampled 

sites to be accounted for, and to add sites as needed. This requires a probability 

sampling approach. Without probability sampling we cannot understand how 

samples represent the “real world’ and are likely to collect biased data that may 

result in incorrect conclusions and inform poor management decisions. Clearly, this 

is vital for effective adaptive management. Furthermore, collecting data under a 

unified probability sampling plan with standardized protocols will greatly increase 

statistical power for the same level of sampling effort, allowing biologists to more 

powerfully analyze large spatial and temporal trends and status. Finally, the 

sampling plan for the Penobscot should be integrated with a larger state-wide 

sampling plan to increase statistical power and optimize the value of limited 

sampling capacity. 

Such surveys are constructed using several components: The Master Sample 

concept is used to unify sampling that is performed by many different entities, such 

as state-wide sampling. It requires 1) sampling from the same frame, and 2) using 

standardized sampling methods. Sampling Frame defines the domain from which 

samples are drawn (e.g. the river network or collection of all river networks in the 

state). Multi-density categories are attributes of the frame that allow the sampling 

design to specify sampling effort based on the attribute (such as stream order). 

Stratification allows the frame to be divided into units of interest for sampling, and 

strata may have differing sampling designs based on needs. Panels allow the 

sampling design to incorporate multi-year designs so rotating samples may be used. 

Oversample allows the sampling design to specify “extra” samples that can be used 

if needed. These samples are consistent with the sampling design. 

Sampling activities in the Penobscot that require a probability sample include 

juvenile salmon surveys (electrofishing or snorkeling), and redd surveys. In addition, 

surveys of habitat characteristics such as water temperature, water quality, or 

habitat features such as large woody debris or stream canopy cover may benefit 

from using probability sampling. 

We used the spsurvey package for R, developed by the US Environmental 

Protection Agency Environmental Monitoring and Assessment Program. This 

package allows the creation of generalized random-tessellation stratified sampling 

PRFP Page 190

designs (GRTS), where samples are regularly distributed in space with known 

inclusion probabilities. Such samples are compatible with standard statistical 

methods (e.g. parametric and non-parametric methods), but statistical methods that 

take advantage of inclusion probability may also be used, such as those in the R 

package psurvey.analysis. We used the Penobscot Basin USGS NHD High GIS 

data as our sampling frame, and developed sampling designs in R. These designs 

can be readily edited to accommodate alternative sampling needs. Further, 

although we focused only on the Penobscot for this exercise, we will create a statewide 

sampling design that integrates the Penobscot sampling plan. This will allow 

the same level of statistically rigorous sampling within the Penobscot basin, but also 

allow the Penobscot data and all other data within the state-wide sampling plan to be 

integrated. A final sampling plan for the Penobscot should be integrated into a 

larger DPS-wide plan, and development of the plan should follow the steps outlined 

later in this document. 

For juvenile survey, we recommend a mix of full population estimates and relative 

abundance estimates performed by electrofishing. Furthermore, additional panels 

could be constructed to formally include CPUE and snorkel samples. 

For redd surveys we recommend developing several index “reaches’ that are 

surveyed every year, preferably multiple times per year to ensure the most accurate 

counts possible, and a multi-panel GRTS design to provide greater spatial coverage. 

Process 

The final sampling plan should follow the process outlined in Figure 1. The plan will 

be constructed to address the various sampling needs to meet the objectives 

defined in the sample design process. 

Figure 1. Flowchart of sampling design development 

source: http://www.epa.gov/nheerl/arm/designpages/designprocoverview5.htm 

PRFP Page 191

The process begins with defining the objectives of the sampling program, and then 

defines the target population(s) and the attribute(s) that are of interest. Next, the 

sampling frame requirements and materials are specified, as are the sampling 

design requirements to meet the objectives. A sampling design and final sampling 

frame are created, and the design is then used to select sampling sites from the 

frame. The results are output as an ESRI shapefile with an attribute table. Overall, 

this must be an iterative process, balancing various sampling objectives with 

achievable sampling effort. There will be a tradeoff between sampling for status and 

trends verses sampling to test specific hypotheses. The objectives must balance 

these competing needs given a certain amount of effort. The sample design should 

also address both short and long term needs. Sampling to assess particular 

management actions may require a very different design than that needed to asses 

naturally reproducing populations. 

Sample Size for Electrofishing 

Sample size and power present many challenges. We have chosen to sample at 

least 5-10 sites per drainage statewide based on the analyses described below 

(also, see Figure 2): 

“We recommend a minimum of 5 – 10 sites be sampled annually within a HUC of 

interest using either multiple pass removal estimates of mean density or mean 

CPUE methodologies. This amount of sampling effort will provide 80% power in 

detecting a trend in the index of abundance for annual rates of change between 0.1 

and 0.2. Although the ability to detect smaller changes is desirable, the amount of 

sampling required to detect such changes greatly increases at annual rates of 

increase less than 0.1 and may not be feasible with limited sampling resources. 

Annual rates of change of 0.1 to 0.2 correspond to approximately a doubling or 

tripling of the index of abundance in a 10 year period. Because of the natural annual 

variation in parr abundance, anything less than a true doubling of abundance may 

be of little to no significance in overall population growth rates of Atlantic salmon.” 

(from J. Sweka, J. Trial, and J. Kocik, draft White Paper on Atlantic Salmon Stock 

Assessment Status and Needs, April 7, 2008.). 

While trend detection is one goal of juvenile assessment, other goals such as 

describing the status of juvenile abundance, or mechanistic relationships between 

environmental variables and juvenile abundance, survival, or growth, are critically 

important. Therefore, the sampling we describe here is a minimum to detect trends 

and describe status, but more in depth sampling may be required for some 

objectives. 

The 5-10 sites will represent annually sampled sites where full population estimates 

are performed. In addition, a rotation of sites that includes CPUE and population 

estimates will be sampled. The design of this will be specific to the drainage, but will 

be based on a three year rotation, where each site will be visited every third year, 

PRFP Page 192

with panels starting in year 1, 2, and 3. A large overage of sites will also be created 

in an attempt to accommodate non-sampling and future sampling needs. 

Required number of sites 

25 

20 

15 

10 

5 

Sample size for 80% power 

0 

0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 

Rate of change per year 

Figure 2. Electrofishing population estimate samples needed to detect a rate 

of change in parr density 

Sample Size for Redd Counts 

Sample size for redd counts should encompass at least 80% of spawning areas 

within a drainage. For the Penobscot, the majority of the basin has not been 

surveyed for spawning habitat. With this in mind, we recommend sampling annually 

at least 80 % of all known spawning habitat, and also surveying a random sample of 

reaches. As knowledge increases about the location of spawning habitat, sampling 

may be modified to take advantage of this. Reaches may be excluded, or added as 

either annual or rotational reaches for sampling. The two objectives are trend 

detection over time, and status of spawning throughout the basin. 

Development of Sampling Design 

The following represents a fully realized juvenile Atlantic salmon probability sample 

for the Penobscot Basin. This provides a real example of the probability design, but 

this particular instance is used to illustrate what a sample focused on trend and 

status would be like. Further refinement in sample size and proportional distribution 

across strata and stream widths is required. Furthermore, integration into a statewide 

sampling plan should be done. The map in Figure 3 shows a sampling design 

with ten annually visited sites per strata, with and additional set of three rotating 

panels of ten sites per year. The samples are also distributed across three stream 

width categories: 0-12 m, 12-24 m, and >24 m. Not shown is a large over-sample 

that was generated to account for additional sites if needed. 

PRFP Page 193

This same sampling design can be used for other sampling needs, such as 

randomly identifying reaches or streams or sites to conduct water quality, water 

temperature, habitat attribute survey, or redd surveys. Sites must simply be chosen 

in the listed order within a stratum to conform to the random sample design. This 

offers flexibility and compatibility with complementary sampling efforts. 



Inaccessible 






Milford to Veazie 


West Enfield to Milford 

Gilman to Stillwater 

Weldon to West Enfield 

Gilman to West Lowell Tannery 

Modeled Habitat 

PenPanel Every Year 

 

Figure 3. Multi-year panel probability sampling design for juvenile Atlantic 

salmon assessment in the Penobscot basin. 

Establishing a sampling design is of paramount importance. This should be 

established before major management activities take place under this plan. The 

program to generate the sampling designs has been created. The next step is to 

PRFP Page 194 

panel 

OverSamp 

Year_1 

Year_2 

Year_3 

Year_Every

incorporate further refinements until the design takes into account the many factors 

that influence sampling in the Penobscot basin. 

Penobscot Watershed Survey Design 

Description of Sample Design for Panel Design 

Target population: All perennial streams/rivers in the Penobscot basin, with the exception 

of the West Branch Penobscot and Webster Brook, which are both inaccessible to 


Sample Frame: GIS stream network coverage from NHD High resolution dataset 

developed by USGS. In addition, Atlantic salmon habitat modeled data based on 

NHD High was used for attribute data. 

Survey Design: A Generalized Random Tessellation Stratified (GRTS) survey design for a 

linear stream resource was used. The GRTS design includes reverse hierarchical 

ordering of the selected sites. 

Multi-density categories: Estimated stream widths based on hydrologic curves: 0-12, 12-24, 

and >24 m. 

Stratification: Stratify by Dam Reaches- portions of the basin sharing the same damrelated 

mortality for migrating smolts and adult Atlantic salmon. 

Panels: Three panels. Year_1 sites will be visited in year 1 and then year 4, year 7, 

etc. Year_2 sites will be visited in year 2, year 5, year 8, etc. Year_3 sites will be 

visited in year 3, year 6, year 9, etc. Year_Every sites will be visited every year. 

Expected sample size: Ten sites per strata annually with an additional 10 rotating sites for a 

total of 20 annually per strata. Sampling distributed across stream width classes as 

"0-12"=15, "12-24"=15, ">24"=10. 

Oversample: 80 sites 

Site Use: The base design has 20 sites per stratum per year. Sites are listed in SiteID 

order and must be used in that order. All sites that occur prior to the last site used 

must have been evaluated for use and then either sampled or reason documented 

why that site was not used. As an example, if 30 sites are to be sampled in the 

stratum, then the first 30 sites in SiteID order would be used. 

Sample Frame Summary 

The total stream length (km) is 9976.5296 km. 

Stream length by Strata and Stream Class 

Stream 

Class 

Above 

Medway 

Brown's Mill 



Stillwater 


West Lowell 

Tannery 


Moosehead 

Manufacturing 

PRFP Page 195

30 NA 108.08662 NA 23.64797 13.455749 

0-6 94.56231 1551.32447 269.754624 314.95553 83.686235 

6-18 12.45829 99.26386 29.218764 35.65461 1.097471 

18-24 8.78391 42.84213 4.493776 37.87435 NA 

24-30 NA 31.43446 18.43036 NA NA 

6-12 8.40795 202.84437 81.619907 62.01569 8.833266 

Sum 124.21246 2035.7959 403.517431 474.14814 107.072721 

Class 

Headwaters 

to Guilford 

Headwaters 



Weldon 


Veazie 

Veazie to Verona 

Island 

>30 14.59095 55.41505 NA 22.3422364 29.41184 

0-6 550.54023 1036.99794 96.5451132 156.4940706 789.92491 

6-18 27.22903 42.39188 0.8700078 0.5296745 61.75123 

18-24 15.43992 11.51391 2.7975842 NA 20.89443 

24-30 11.77406 11.65105 NA NA 32.77084 

6-12 50.8037 137.29964 12.5826661 20.1374415 240.40878 

Sum 670.37789 1295.26947 112.7953713 199.503423 1175.16202 

Class 


West Enfield 

West Ernfield 

to Milford Sum 

>30 97.26506 8.36267 372.5781 

0-6 2165.72194 342.19826 7452.7056 

6-18 117.4552 36.09102 464.011 

18-24 57.86753 16.40395 218.9115 

24-30 18.61077 15.69942 140.371 

6-12 374.26756 128.73143 1327.9524 

Sum 2831.18806 547.48675 9976.5296 

Site Selection Summary 

Number of Sites 

mdcaty OverSamp Year_1 Year_2 Year_3 Year_Every Sum 

0-12 310 45 38 33 39 465 

12-24 293 35 41 41 35 445 

>24 197 20 21 26 26 290 

Sum 800 100 100 100 100 1200 

Description of Sample Design Output: 

The sites are provided as a shapefile that can be read directly by ArcMap. The dbf 

file associated with the shapefile may be read by Excel. 

The dbf file has the following variable definitions: 

Variable Name Description 

SiteID Unique site identification (character) 

arcid Internal identification number 

x Albers x-coordinate 

y Albers y-coordinate 

mdcaty Multi-density categories used for unequal probability selection 

weight Weight (in meters), inverse of inclusion probability, to be used 

PRFP Page 196

in statistical analyses 

stratum Strata used in the survey design 

panel Identifies base sample by panel name and Oversample by 

OverSamp 

auxiliary variables Remaining columns are from the sample frame provided 

Projection Information 

No projection information available. Uses the projection of the ArcMap project. 

Evaluation Process 

The survey design weights that are given in the design file assume that the survey 

design is implemented as designed. That is, only the sites that are in the base 

sample (not in the over sample) are used, and all of the base sites are used. This 

may not occur due to (1) sites not being a member of the target population, (2) 

landowners deny access to a site, (3) a site is physically inaccessible (safety 

reasons), or (4) site not sampled for other reasons. Typically, users prefer to 

replace sites that can not be sampled with other sites to achieve the sample size 

planned. The site replacement process is described above. When sites are 

replaced, the survey design weights are no longer correct and must be adjusted. 

The weight adjustment requires knowing what happened to each site in the base 

design and the over sample sites. EvalStatus is initially set to “NotEval” to indicate 

that the site has yet to be evaluated for sampling. When a site is evaluated for 

sampling, then the EvalStatus for the site must be changed. Recommended codes 

are: 

EvalStatus 

Code 

Name Meaning 

TS Target Sampled site is a member of the target population and was 

sampled 

LD Landowner Denial landowner denied access to the site 

PB Physical Barrier physical barrier prevented access to the site 

NT Non-Target site is not a member of the target population 

NN Not Needed site is a member of the over sample and was not 

evaluated for sampling 

Other codes Many times useful to have other codes. For example, 

rather than use NT, may use specific codes indicating 

why the site was non-target. 

Statistical Analysis 

Any statistical analysis of data must incorporate information about the monitoring 

survey design. In particular, when estimates of characteristics for the entire target 

population are computed, the statistical analysis must account for any stratification 

or unequal probability selection in the design. Procedures for doing this are 

available from the Aquatic Resource Monitoring web page given in the bibliography. 

A statistical analysis library of functions is available from the web page to do 

common population estimates in the statistical software environment R. 

For further information, contact 

Gregory Mackey 

Fisheries Scientist 

Bureau of Sea Run Fisheries and Habitat 

PRFP Page 197

Maine Department of Marine Resources 

Regular Mail 

172 State House Station 

Augusta, Maine 04333 

UPS/Fed Express 

6 Beech Street 

Hallowell, Maine 04347 

(207) 624-6358 voice 

(207) 287-9975 fax 

Bibliography: 

Stevens, Jr., D. L., D. P. Larsen, and A. R. Olsen. 2007. The role of sample 

surveys: Why should practitioners consider using a statistical sampling design? in D. 

H. Johnson, B. M. Shrier, J. S. O’Neal, J. A. Knutzen, X. Augerot, T. A. O’Neal, and 

T. N. Pearsons. Salmonidfield protocols handbook: techniques for assessing status 

and trends in salmon and trout populations. American Fisheries Society, Bethesda, 

Maryland. 

Stevens, D. L., Jr., and A. R. Olsen. 2004. Spatially-balanced sampling of natural 

resources in the presence of frame imperfections. Journal of American Statistical 

Association. 99. 262-278. 

Hayes, D., E. Baker, R. Bednarz, D. Borgeson, Jr., J. Braunscheidel, J, Breck, M. 

Brennigan, A. Harrington, R. Hay, R. Lockwood, A. Nuhfer, J. Schneider, p. 

Seelbach, J. Waybrant, and T. Zorn. 2003. Developing a standardized sampling 

program: The Michigan experience. Fisheries. 28. 18-25. 

Diaz-Ramos, S., D. L. Stevens, Jr, and A. R. Olsen. 1996. EMAP Statistical Methods 

Manual. EPA/620/R-96/002, U.S. Environmental Protection Agency, Office of 

Research and Development, NHEERL-Western Ecology Division, Corvallis, Oregon. 

Web Page: http://www.epa.gov/nheerl/arm 

PRFP Page 198

Appendix I – Downstream Passage Studies for Atlantic Salmon 

Author: Norm Dubé 

RESULTS OF DOWNSTREAM PASSAGE 

STUDIES FOR ATLANTIC SALMON, 

PENOBSCOT RIVER, MAINE 

MATTACEUK (WELDON) (FERC No. 2520) 

Project Description 

Project Works: 657’ long x 40’ high ogee spillway including 4’ high flashboards; 

roller gate 90’ long x 19’ high to control spills and headpond levels. 

Turbines: 4 Turbine Type: 2 fixed blade, 2 Kaplan 

Generating Capacity: 19.2 MW 

Hydraulic Capacity: 7,000 cfs 

Downstream Passage System 

Years Studied: 1987 – 1999 Life Stages Studied: smolts, kelts 

Permanent Bypass System: 1) single surface inlets integral with trashracks on two 

of four turbine forebays for fish collection; 2) strobe lights in remaining two forebays 

for fish repulsion; 3) one-inch clear spacing overlay trashracks to depth of 16 feet at 

full pond at all four turbine intakes to discourage fish entrainment; 4) a 42-inch 

underground fish passage pipe for transport of collected fish to the tailrace area. 

System installed in 1992. 

Study Methods: Radio telemetry; in-line monitoring facility at passage pipe 

Collection Efficiency: Smolts -17% - 59%; six years combined – 38% (N = 155) 

Kelts – 63% (fall studies, three years, N = 8) 

Kelts – 76% (spring studies, three years, N = 25) 

Turbine Survival: Not studied; estimated at 1) 95% for smolts (Truebe, J. and M. 

Drooker. 1985. A Summary of State of the Art Methods for Passage of Downstream 

Migrating Salmon With Application to the Great Northern Paper Weldon Station, 

Mattaceunk Project, Penobscot River, Maine. FERC No. 2520), and 2) 90% (acute 

mortality 10%, smolts, ASAL Model). 

Downstream Passage Routes: spillway, roll gate, log sluice, fixed blade propeller 

turbines (2), Kaplan turbines (2), downstream passage system. 

PRFP Page 199

WEST ENFIELD (FERC No. 2600) 


Project Works: 363’ long x 39’ high ogee spillway plus 6’ high flashboards; 45’ long 

non-overflow spillway; 107’ long gated spillway. 

Turbines: 2 Turbine Type: Pit Type (horizontal Kaplan turbines) 

Generating Capacity: 13 MW 



Years Studied: 1990 – 1994 (smolts) Life Stages Studied: smolts; kelts 

1990 (kelts) 

Permanent Bypass System: weirs (5) plus transport flume; system installed when 

project redeveloped in 1988. 

Study Methods: radio telemetry 

Collection Efficiency: Smolts -2% - 36%; five years combined – 17% (N = 259) 

Kelts – 4% (spring study, N = 23) 

Turbine Survival: 97.7% (acute mortality 2.3%, smolts, Shepard 1993); estimated 

at 95% (acute mortality 5%, smolts, ASAL Model). 

Downstream Passage Routes: turbines, downstream passage system, spillway, 

and gates 

PRFP Page 200

MILFORD (FERC No. 2534) 


Project Works: 1,159’ long x 20’ high concrete gravity spillway plus 4.5’ high 

flashboards; 25’ wide concrete sluiceway and gate. 

Turbines: 4 Turbine Type: Kaplan (3); fixed blade (1) 

Generating Capacity: 6.4 MW 




1988 – 1989 (kelts) 

Permanent Bypass System: No dedicated downstream bypass system at time of 

studies; angled rack guidance system to direct downstream migrants to and through 

an empty turbine pit has since been deployed. System has not been studied. 


Collection Efficiency: Smolts – N/A; 41% turbine passage; 59% spillway passage; 

(N = 68) 

Kelts – N/A; 100% spillway passage; spring studies only, 

(N = 30) 

Turbine Survival: Not studied; estimated at 91% (acute mortality 9%, smolts, ASAL 

Model). 

Downstream Passage Routes: turbines, spillway, gates, and downstream passage 

system 

PRFP Page 201

VEAZIE (FERC No. 2403) 


Project Works: 902’ long x 25’ high concrete buttress spillway including 6.5’ 

Obermeyer inflatable flashboard system; approximately 240’ long x 25’ high concrete 

forebay including 3.5’ (approximate) high fixed flashboards. 

Turbines: 15 (Station A); 2 (Station B) Turbine Type: Station A: vertical Francis 

(15); Station B: vertical fixed blade (2) 

Generating Capacity: 5.4 MW (Station A); 3.0 MW (Station B) 




1988 – 1989 (kelts) 

Permanent Bypass System: No dedicated downstream bypass system; attempts 

have been made to utilize trash gate/ice sluice as downstream bypass route for 

smolts with limited success. Studies were undertaken when main spillway had 6.5’ 

hinged wooden flashboards (i.e. prior to installation of Obermeyer system). 


Collection Efficiency: Smolts – N/A; 29% turbine passage; 71% spillway/ice sluice 

passage; (N = 42) 

Kelts – N/A; 100% spillway passage; spring studies only 

(N = 30) 

Turbine Survival: Not studied; estimated at 91% (acute mortality 9%, smolts, ASAL 

Model). 

Downstream Passage Routes: turbines, spillway, forebay, trash gate, and ice 

sluice 

Note: downstream passage data collected for other projects in the lower Penobscot 

system (Stillwater, Orono, Great Works) but did not study specific downstream 

passage routes, rather only monitored passage by the project. 

DOWNSTREAM PASSAGE STUDIES AT HYDROPOWER DAMS, PENOBSCOT 

RIVER, MAINE, 1987-1999 

(Atlantic Salmon) 

PRFP Page 202

Bangor-Pacific Hydro Associates. 1993. 1992 Evaluation of Downstream Fish 

Passage Facilities at the West Enfield Project (FERC No. 2600). 11 pp. + 

Appendices. 



Appendices. 



Appendices. 

Great Northern Paper, Inc. 1987. 1987 Report on Downstream Passage of Atlantic 

Salmon Smolts and Kelts at Weldon Dam. Mattaceunk Project, FERC No. 2520. 

Great Northern Paper, Inc., Millinocket, Maine. 32 pp. + Appendices. 


Salmon Smolts and Kelts at Weldon Dam. Great Northern Paper, Inc., Millinocket, 

Maine. x + 90 pp. + Appendices. 



Maine. xi + 94 pp. + Appendices. 



Maine. 10 pp. + Appendices. 

Great Northern Paper, Inc. 1992. 1991-1992 Report on the Effectiveness of Interim 

Downstream Passage Facilities for Atlantic Salmon Smolts and Kelts at Weldon 

Dam. Mattaceunk Project. FERC No. 2520. Great Northern Paper, Inc., Millinocket, 

Maine. vi + 22 pp. + Appendices. 

Great Northern Paper, Inc. 1993. 1993 Report on the Effectiveness of Permanent 

Downstream Passage Facilities for Atlantic Salmon at Weldon Dam. Mattaceunk 

Project. FERC No. 2520. Great Northern Paper, Inc., Millinocket, Maine. ii + 54 pp. + 

Appendices. 


Downstream Passage Facilities for Atlantic Salmon at Weldon Dam. Mattaceunk 

Project. FERC No. 2520. Great Northern Paper, Inc., Millinocket, Maine. ii + 61 pp. + 

Appendices. 

Great Northern Paper, Inc. 1995. 1995 Report on the Effectiveness of the 

Permanent Downstream Passage System for Atlantic Salmon Weldon Dam. 

PRFP Page 203

Mattaceunk Project. FERC No. 2520. Great Northern Paper, Inc., Millinocket, Maine. 

ii + 78 pp. + Appendices. 


Permanent Downstream Passage System for Atlantic Salmon at Weldon Dam. 

Mattaceunk Project. FERC No. 2520. Great Northern Paper, Inc., Millinocket, Maine. 

ii + 61 pp. + Appendices. 


Permanent Downstream Passage System for Atlantic Salmon at Weldon Dam. Great 

Northern Paper, Inc., Millinocket, Maine. iii + 36 pp. + Appendices. 


Downstream Passage Facilities for Atlantic Salmon Weldon Dam. Mattaceunk 

Project, FERC No. 2520. Great Northern Paper, Inc., Millinocket, Maine. 32 pp. + 

Appendices. 

Hall, S.D. and S.L. Shepard. 1990a. 1989 Progress Report of Atlantic Salmon Kelt 

Radio Telemetry Investigations on the Lower Penobscot River. Bangor Hydro- 

Electric Co., Bangor, Maine. 30 pp. 

Hall, S.D. and S.L. Shepard. 1990b. Report for 1989 Evaluation Studies of 

Upstream and Downstream Facilities at the West Enfield Project (FERC No. 2600). 

Bangor-Pacific Hydro Associates. 17 pp. + Appendices. 

Shepard, S.L. 1988. 1988 Progress Report: Atlantic Salmon Kelt Radio Telemetry 

Investigations in the Lower Penobscot River. Bangor Hydro-Electric Co., 32 pp. + 

Appendices 

Shepard, S.L. 1991a. Report on Radio Telemetry Investigations of Atlantic Salmon 

Smolt Migration in the Penobscot River. Bangor Hydro-Electric Co., 38 pp. + 

Appendices. 

Shepard, S.L. 1991b. Evaluation of Upstream and Downstream Fish Passage 

Facilities at the West Enfield Project (FERC No. 2600). Bangor-Pacific Hydro 

Associates, 25 pp. + Appendices. (Note: fall 1989 and spring 1990 studies). 

Shepard, S.L. 1991c. Evaluation of Upstream and Downstream Fish Passage 

Facilities at the West Enfield Project (FERC No. 2600). Bangor-Pacific Hydro 

Associates, 27 pp. + Appendices. (Note: spring and fall 1991 studies). 

Shepard, S.L. 1993. Survival and Timing of Atlantic Salmon Smolts Passing the 

West Enfield Hydroelectric Project. Bangor-Pacific Hydro Associates. 27 pp. 

PRFP Page 204

Shepard, S.L. and S.D. Hall. 1991. Final Report: Adult Atlantic Salmon Radio 

Telemetry Studies in the Penobscot River. Bangor Hydro-Electric Co., 49 pp. + 

Appendices. 

PRFP Page 205

Appendix J – Northern Pike Risk Assessment for Piscataquis River 

Authors: Melissa Laser (editor), Fred Seavey (USFWS), Richard Dill (MDIFW), Merry Gallagher (MDIFW), Tim 

Obrey (MDIFW), Jeff Reardon (Penobscot Trust), Rory Saunders (NOAA), Tara Trinko (NOAA) 

Introduction 

The Penobscot River is New England's second largest river, with a watershed that 

covers about a third of the State of Maine (approximately 22,300 km 2 ; 8,600 mi 2 ). It 

is 563 km long (350 miles) and has a total fall of 488 m (1,770 feet) from its highest 

point, Penobscot Lake. There are diverse aquatic environments in the watershed 

with over 2,575 km (1,600 miles) of streams and rivers and more than 625 lakes and 

ponds with a total surface area of 103,036 ha (254,600 acres). For thousands of 

years, diadromous fishes migrated through much of the basin, providing a 

connection between the Gulf of Maine and inland terrestrial and aquatic ecosystems. 

Since 1959, multiple reports have documented the issues facing diadromous fish 

restoration in the Penobscot drainage. 

In 2006, the Maine Departments of Inland Fisheries and Wildlife (MDIFW) and 

Marine Resources (MDMR) began work on a strategic plan to restore diadromous 

fish in support of the Penobscot River Restoration Project (PRRP). The overarching 

goal of the Penobscot River diadromous fish restoration strategy is to restore and 

guide the management of diadromous fish populations, aquatic resources and the 

ecosystems on which they depend, for their intrinsic, ecological, economic, 

recreational, scientific, and educational values for use by the public. At least 85 

species of fish inhabit the Penobscot River basin (Baum 1983). Thirty-five are found 

in marine or estuarine waters, 33 occur in freshwater, five species tolerate a range of 

salinities, and 12 are diadromous species that migrate between marine and 

freshwater habitats. All of the fishes are native to Maine with the exception of eight 

freshwater species. Since 1983, black crappie, green sunfish, largemouth bass, 

central mudminnow, white catfish, and northern pike have been illegally introduced 

into the Penobscot basin. Brown trout, an exotic species native to Europe, is 

currently stocked by MDIFW for recreational fishing in one body of water located 

above a set of falls impassable to all species of fish but Atlantic salmon. Chain 

pickerel and smallmouth bass, managed by MDIFW as sportfish, were introduced 

into Maine waters in the 1800s and have been spread legally and illegally throughout 

the basin. Landlocked salmon, rainbow smelt, lake trout and white perch are native 

to the Penobscot basin, but their range has been artificially expanded. This 

restoration strategy focuses on native diadromous fishes, which are all currently at 

less than 1% of historic levels. 

Northern pike is a non-native invasive species that has high potential for negative 

ecological impacts on native species. Management objectives to contain or eradicate 

this species within the Penobscot watershed may be in direct conflict with the 

objectives of the diadromous fish restoration strategy. This conflict is most apparent 

in actions relating to fish passage. The Howland by-pass, one aspect of the PRRP, 

will allow diadromous species access to the Piscataquis drainage but also opens the 

drainage to natural dispersal of northern pike. 

PRFP Page 206

Options under the Multiparty Settlement Agreement (MPA) were a bypass channel 

without trap and sort facilities, or removal of the dam. Construction of the bypass 

channel rather than dam removal was the preferred alternative by the restoration 

parties as engineering design and hydraulic modeling showed a bypass channel 

could be constructed and provide free-swim upstream and downstream passage at 

the Howland dam, rather than necessitating dam removal. Thorough evaluation and 

engineering design of trap and sort facilities to prevent further upstream movements 

of pike into the Piscataquis River drainage through the bypass channel 

were conducted concurrently. This evaluation determined trap and sort facilities to 

be unfeasible in meeting restoration goals. 

The fisheries agencies and other parties agreed to undertake a formal risk 

assessment of potential pike movements through the channel and into upstream 

sub-drainages. This risk assessment seeks to document the timeline of events 

relating to the documentation of pike and the PRRP, the ecological risk of pike on 

native species, patterns of natural dispersal and human introductions, and focus 

areas for action. The section concludes with management actions to reduce the 

impact of pike above the Howland bypass. 

Background 

In June 2004, PPL Corporation (PPL), state and federal resource agencies, the 

Penobscot Indian Nation (PIN), and various NGOs, signed the Lower Penobscot 

River Multiparty Settlement Agreement (MPA), which led to the Penobscot River 

Restoration Project (PRRP). This unprecedented and historic agreement provides 

the Penobscot River Restoration Trust (Trust), a non-profit organization, the option 

to purchase three dams from PPL, decommission and remove the two lowermost 

dams on the main stem of the river (Veazie and Great Works), and decommission 

and pursue construction of an innovative experimental fish bypass around the 

Howland dam, located upstream on the Piscataquis River. 

Under the Multi Party Agreement (MPA), the Trust was required to seek a “prior 

determination” by the U.S. Fish and Wildlife Service, the Maine Departments of 

Inland Fisheries and Wildlife and Marine Resources, the Maine Atlantic Salmon 

Commission, and the PIN that the proposed bypass “will provide safe, timely, and 

effective fish passage sufficient to allow the fisheries management goals and 

objectives of the Resource Agencies and PIN to be met.” 

During the design process, in consultation with the fisheries agencies, the Trust 

developed an “Outline for Preliminary Design of Proposed Howland Fish Bypass”, 

which describes the information needed by the agencies to make their “prior 

determination.” At the request of several agencies, this included the following: 

The preliminary design will also evaluate the feasibility and costs (including 

operating costs) of incorporating provisions for trapping/sorting/counting of 

fish using the bypass. This includes measures to exclude upstream migration 

of northern pike and black crappie, both of which do not now exist above the 

PRFP Page 207

Howland Dam, and are considered by Maine Department of Inland Fisheries 

and Wildlife to be undesirable, non-native invasive species. Under the terms 

of the Settlement Agreement, the resource agencies are responsible for 

management activities such as trapping/sorting/trucking. 

To fulfill that requirement, Milone and MacBroom, the Trust’s design consultant, subcontracted 

with Stantec to complete an evaluation of the feasibility and potential 

costs of incorporating a trap and sort facility into the bypass channel. Stantec’s final 

report is attached. (Appendix A: Trapping/Sorting/Counting Facility Proposed 

Bypass Channel Howland Dam, Howland, Maine. May 20, 2008.) In addition to 

completing the report, Stantec also participated with the Trust in a meeting attended 

by representatives of the US Fish and Wildlife Service, NOAA Fisheries, Maine 

Department of Marine Resources, Maine Department of Inland Fisheries and 

Wildlife, and the Penobscot Indian Nation on March 24, 2008 to discuss the 

feasibility of trapping and sorting. A handout summarizing Stantec’s evaluation was 

distributed at the meeting and is included as Appendix B. The handout summarizes 

information presented in more detail in the May 20 report. 

As a result of Stantec’s work and consultation with the agencies, the Trust 

determined that a trapping and sorting facility at the Howland Bypass could be 

designed and constructed, at an additional construction cost of $250,000 to 

$500,000, and with annual maintenance and operations costs of $75,000 to 

$300,000. The number of returning alewives would largely drive the maintenance 

and operations costs as the most abundant species anticipated. In consultation with 

the state and federal fisheries agencies, the Trust, as well as the state and federal 

fisheries agencies who had been consulted on this matter, determined that installing 

a trapping and sorting facility in the bypass channel would not be feasible, because: 

(1) A trap and sort facility would require design changes to the proposed bypass 

channel that would likely reduce its effectiveness in passing target species, 

which, under the terms of the MPA, would make the bypass channel “not 

feasible” and require the Trust to seek dam removal. 

(2) It was unlikely that the facility could be 100% effective in preventing 

undesirable species, including northern pike, from passing the Howland Dam, 

because of uncertainty about the swimming capacity of northern pike and 

concerns that required manual sorting would be subject to error due the large 

number of fish that would need to be handled. In addition, a trap and sort 

facility would do nothing to address what is probably the most potential vector 

for pike introduction into the Piscataquis—illegal introductions. The presence 

of multiple dams in the Androscoggin, Kennebec, and Sebasticook 

watersheds has not prevented introduction of pike into multiple waters there; 

(3) The proposed trap and sort facility would have negative impacts on target 

species, including migratory delays, required handling of all fish passed, 

potential injuries to fish that attempted to leap the barrier, crowding, and the 

need for a separate eel passage facility; 

(4) Annual maintenance and operations costs would be prohibitive, particularly as 

the number of returning alewives increased. 

PRFP Page 208

As a result of the discussion at the March 24 meeting, the Trust submitted 

Preliminary Design Plans for the Howland Bypass that did not include a trap and sort 

facility for the agencies review, and requested a letter from each agency containing 

its “prior determination” that the proposed bypass channel would meet each 

agency’s needs. The Trust received a letter on June 17, 2008 from NOAA Fisheries, 

and on June 18, 2008 from the Penobscot Nation, the U.S. Fish and Wildlife Service, 

and the State of Maine (on behalf of the Maine Department of Inland Fisheries and 

Wildlife, the Maine Department of Marine Resources, and the Maine Atlantic Salmon 

Commission). All state and federal agencies concurred in the design of the 

bypass—which did not include a trap and sort facility. 

The letter from the State of Maine stated that: 

“The State resource agencies do have concerns about the impact of invasive fish 

species such as northern pike that are found in the lower reaches of the Penobscot. 

The agencies have agreed not to require a trap-and-sort facility at the proposed 

Howland Bypass, however ongoing strategic and operational planning may identify 

the need for additional upstream barriers to prevent the spread of invasive fish 

species into native salmonid habitat.” 

Timeline 

Action Plan For Managing Invasive Aquatic Species 

In the late 1990s, concerns over invasive plants and nuisance species in Maine 

began to grow with the introduction of milfoil into several waters in southern Maine. 

There were also an increasing number of illegal introductions of fish species, 

particularly northern pike, black crappie, smallmouth bass and largemouth bass in 

many waters in southern and central Maine. 

In response, the 120 th Maine State Legislature passed legislation establishing an 

interagency task force on invasive plants and nuisance species. This committee 

contains 17 members including the commissioners of the following State agencies: 

Environmental Protection, Inland Fisheries and Wildlife, Health and Human 

Services, Agriculture, Food and Rural Resources, and Conservation. Twelve 

additional public members of the committee with expertise or interest in this area are 

appointed by the governor. The task force was charged with making 

recommendations to the Land and Water Council on the following subjects: 

A. The importation and transportation of invasive aquatic plants and nuisance 

species. 

B. Monitoring and educational programs aimed at the control of invasive 

aquatic plants and nuisance species. 

C. A comprehensive state invasive aquatic plants and nuisance species 

management plan that meets the requirements of the National Invasive 

Species Act of 1996. 

D. A statewide inventory of invasive aquatic plants and nuisance species. 

PRFP Page 209

E. Methods to improve cooperation of state, provincial, federal and 

nongovernmental agencies in the area of invasive aquatic plants and 

nuisance species. 

F. Recommendations on the feasibility of implementing lake protection 

assessment districts that allow residents and owners of land within 250 

feet of inland waters to assess themselves to raise funds in the 

prevention and control of invasive aquatic plants. 

G. Other recommendations as necessary to control the introduction of 

invasive aquatic plants and nuisance species in the State. 

The task force was also directed, through this legislation, to cooperate with 

representatives from federal, state and local agencies and private environmental and 

commercial interests in the northeastern United States to form a northeastern 

regional panel to establish priorities and coordinate activities to prevent the spread 

of milfoil and other invasive aquatic plants and nuisance species in the Northeast. In 

October 2002, the task force finalized its’ comprehensive action plan for managing 

invasive species. The action plan notes that Maine must be vigilant to prevent 

further introductions of exotic species which can displace native species, reduce 

biodiversity, disrupt food webs, and degrade habitats. The action plan lists all 

species identified by the task force as undesirable, exotic, invasive species; northern 

pike are included. The action plan directed the Departments of Environmental 

Protection and Inland Fisheries and Wildlife to establish a Rapid Response plan for 

the introduction of invasive fish species. The rapid response plan was signed in 

2006. 

Penobscot River Restoration Project and Pushaw Lake 

Discussions for possible removal of one or more lower Penobscot River dams to 

facilitate anadromous fisheries restoration began in the early and mid 1990s during 

deliberations about the proposed new Basin Mills Hydroelectric Project at Orono. 

In 1997, formal USDOI fish passage prescriptions for the lower Penobscot 

River dams (Veazie, proposed Basin Mills, Orono, Stillwater, Milford) were filed with 

the Federal Energy Regulatory Commission (FERC). Following these events, 

various options for anadromous restoration were the subject of discussions between 

then owner of the dams Bangor Hydro Electric Company, State and Federal 

fisheries agencies, PIN, and a coalition of conservation organizations and other 

interested parties. 

ASAL population modeling for restoration of Atlantic salmon was undertaken during 

review of the proposed Basin Mills Project. This modeling indicated that incremental 

losses due to passage inefficiencies at multiple dams, even with state-of-the-art 

upstream and downstream fish passage facilities, would make it very difficult to 

achieve restoration or maintain a viable salmon population based upon natural 

recruitment alone. According to the model, removal of dams to provide unrestricted 

passage and reduce these losses greatly improved chances of successful 


PRFP Page 210

By 2000, PPL (new owner of the dams), PIN, State and Federal fisheries agencies 

and the coalition were continuing discussions on restoration, fish passage and 

related requirements under the FERC licenses. The Howland Dam (Piscataquis 

River) and Enfield Dam (mainstem Penobscot River) were now included. Howland 

was due for FERC relicensing in 2000 (a new license application was filed in 1998 

and under review). Fish passage efficiency studies were being required for the 

existing Howland Dam fishway. All parties remained interested in possible reduction 

of the number of dams to reduce upstream and downstream passage losses 

and facilitate restoration potential. 

Over the next two years serious development continued toward a collaborative 

Conceptual Settlement Agreement to address Penobscot River fisheries restoration. 

Possible removals of the Veazie and Great Works dams were on the table, as was 

consideration of a bypass channel or dam removal at Howland. PPL, Federal and 

State fisheries agencies, PIN, Penobscot Coalition all remained engaged and 

committed to restoration goals. 

In 2003, a Conceptual Agreement was finalized by the parties. It provided the 

framework for development of a more detailed settlement agreement to fully address 

restoration plans and fish passage issues at the multiple dams. It included 

consideration of a bypass channel at Howland capable of providing free-swim, 

unrestricted upstream passage for Atlantic salmon, shad and alewives. At this time 

black crappies in the Souadabscook drainage were the only confirmed invasive 

species in the lower Penobscot. 

In April 2004, the Multiparty Settlement Agreement was finalized. It formalized plans 

for removal of the Veazie and Great Works dams, and for evaluation of a possible 

bypass channel at Howland. Any bypass channel had to be capable of providing 

unrestricted upstream passage for restoration species. If a free-swim bypass 

channel could not be designed or constructed the alternative to provide passage at 

Howland was dam removal. State of the art fishways or fish lifts were expressly not 

considered acceptable at Howland. 

In the summer of 2003 there had been an unconfirmed report of a northern pike 

being angled at Pushaw Lake, but the fish was not available for examination or 

species confirmation. A second angled pike was reported from Pushaw in the 

summer of 2004. This time the fish (head only) was made available for examination 

by MDIFW biologists and confirmed to be a northern pike. A second pike was 

caught and confirmed in January 2005. No pike were found by electrofishing 

surveys of Pushaw Stream and the lower mainstem Penobscot River during summer 

2005. In June of 2006 two different anglers reported catching a northern pike in the 

Penobscot River. The first was near the confluence of Pushaw Stream to the 

Penobscot River in Old Town, the second report was from just down river of the 

Howland Dam. These reports prompted a temporary emergency closure of both the 

Howland and West Enfield fishways. With advice from USFWS engineers, both 

fishways were modified to include a vertical jump of no less than 30 inches in order 

PRFP Page 211

to preclude the upstream passage of pike in the drainage. Renowned fisheries 

scientist and expert on Northern pike, Dr. John Casselman, agreed that a 30-inch 

jump is adequate to prevent the upstream passage of pike through the fishways 

(pers. comm.). 

After the confirmation of the presence of northern pike, a lake management plan was 

developed with the main goal of preventing further spread of the invasive and 

controlling the population in Pushaw Lake (Gallagher et al. 2006). The Pushaw Lake 

management plan also examined methods for potentially eliminating or suppressing 

the pike population in Pushaw Lake. The plan noted that the large lake with 

considerable wetlands and residential development would be unsuitable for chemical 

reclamation. Several barrier methods were considered for the outlet but none were 

deemed feasible for a variety of reasons. The plan concludes that eradication of pike 

from Pushaw is unlikely, but that suppression or control methods should be explored 

and have been underway since 2006. 

Spring removal efforts have been conducted for three years (2006-08) with some 

success. So far, there has not been a dramatic increase in the pike population at 

Pushaw Lake as evident by the low capture rate of pike by anglers. To date records 

indicate 60 female pike have been removed in 3+ years through angling and spring 

trap netting. The total pounds of females removed is ~ 300 which translates into 

about three million eggs (~ 10,000 eggs per pound of body weight). 

Following confirmation of northern pike in Pushaw Lake, and the 

recognized potential for upstream migration, the parties to the MPA agreed to 

undertake an evaluation for feasibility of creating a fish passage barrier and trap and 

sort capability within any bypass channel to be constructed at Howland. Extensive 

hydraulic engineering and modeling was underway (by the Trust) to determine if a 

bypass channel capable of unrestricted upstream passage for restoration species 

could in fact be designed. 

Accordingly, USFWS fishway design engineers and passage experts at the Conte 

Lab provided detailed evaluation. From that evaluation it was determined that 

any benefits of a bypass channel to provide free-swim migration for restoration 

species would be completely negated by measures necessary to provide assurance 

of near-100% exclusion of pike. Extensive additional excavation of the channel and 

an elaborate upstream barrier dam and trap and sort facilities would be required. In 

addition, notwithstanding the high cost of construction and ongoing operation, even 

the most effective trap and sort operation possible at this site was considered 

to cause unacceptable delay in migration of the various restoration species. Under 

the MPA, if a free-swim bypass channel could not be constructed the 

alternative was breach or removal of the Howland Dam. 

The agencies and restoration interests agreed the best alternative (rather than 

breaching or removing the Howland dam) would be to undertake a risk assessment 

for upstream pike movements and to evaluate existing or potential upstream 

PRFP Page 212

arriers to prevent movement of pike into sensitive sub-drainages, resulting in this 

document. 

Ecological Risk 

Miller et al (1989) estimated that exotic introductions were responsible for 68% of 

fish extinctions in North America. Introductions of large, top-predators such as 

northern pike (Esox lucius) negatively affect resident fish communities by disrupting 

normal feeding behavior (Bystrom et al. 2007), decreasing prey biomass and 

abundance (He and Kitchell 1990; Findlay et al. 2005) and through extirpation of 

native species (Findlay et al. 2005; Bystrom et al. 2007). 

Northern pike introductions in Maine 

Northern pike were initially introduced into Maine in the 1970s, as the result of an 

illegal introduction into the Belgrade Chain of Lakes (Brautigam 2001). Subsequent 

migration within the Belgrade Lakes drainage and additional illegal introductions are 

responsible for an expanding distribution within central and southern Maine, which 

until the 1990s was limited to two river drainages, the Androscoggin and the 

Kennebec. Since 1985, the number of northern pike waters has increased from six 

to 49 (with 17 expected and one extirpated) statewide (Lucas 2008), representing 

72,789 acres in lake surface area (Table 1). In 2004, northern pike were confirmed 

in Pushaw Lake in the Penobscot River drainage (Gallagher et al. 2006), effectively 

giving northern pike access to over 100 river kilometers in the Penobscot mainstem 

from the mouth of the river to the Howland and West Enfield dams. Portions of the 

upper watershed are also accessible if pike are able to use the existing fishways 

installed at the upper dams. 

Table 1. Waterbodies with reported pike occurrences 

County Year Lake Town Confirmed Status 

Kennebec 1980 Great Pond Belgrade Y Present 

Kennebec 1980 Ingham Pond Mount Vernon Y Present 

Kennebec 1980 Long Pond Belgrade Y Present 

Kennebec 1980 Messalonskee Lake Belgrade Y Present 

Kennebec 1980 Belgrade Stream Belgrade Y Present 

Kennebec 1980 Great Meadow Stream Belgrade Y Present 

Oxford, Coos (NH) 1990 Umbagog Lake Magalloway Plt Y Present 

Kennebec, Somerset 1980 North Pond Rome Y Present 

Androscoggin 1994 Sabbatus Pond Greene Y Present 

Kennebec 1996 Berry Pond Winthrop Y Present 

Kennebec 1996 Dexter pond Winthrop N Present 

Kennebec 1996 Cobbosseecontee Lake Winthrop Y Present 

Kennebec 1996 Annabessacook Lake Monmouth Y Present 

Kennebec 1996 Lower Narrows Pond Winthrop Y Present 

Kennebec 1996 Upper Narrows Pond Winthrop N Present 

Kennebec 1996 Horseshoe Pond Litchfield N Present 

Kennebec 1996 Pleasant Pond Gardiner N Present 

Kennebec 1996 Wilson Pond Wayne N Present 

Somerset 1998 Androscoggin River Bethel Y Present 

PRFP Page 213

Kennebec 1998 Rome Trout Brook Rome Y Present 

Androscoggin 1999 Taylor Pond Auburn Y Present 

Androscoggin, Oxford 1999 Bear Pond Hartford Y Present 

Oxford 1999 Little Bear Pond Hartford Present 

Androscoggin 2000 Crystal Pond Turner N Present 

Androscoggin 2000 Little Sabbattus Pond Greene Y Present 

Kennebec 2000 Moose Pond Stream Mount Vernon Y Present 

Kennebec 2000 Stony Brook Mount Vernon Y Present 

Androscoggin 2000 Androscoggin River Turner Y Present 

Sagadahoc 2001 Winnegance Lake Phippsburg Y Present 

Androscoggin 2002 Long Pond Livermore Y Present 

Kennebec 2002 Torsey Pond Mount Vernon Y Present 

Kennebec 2002 Webber Pond Vassalboro N Present 

Lincoln 2002 Biscay Pond Damariscotta N Present 

York 2002 Middle Branch Pond Waterboro Y Present 

Waldo 2002 Sheepscot Pond Palermo N Present 

York 2002 Estes Lake Sanford Present 

Penobscot 2003 Pushaw Lake Alton Y Present 

Cumberland 2003 Sebago Lake Sebago Y Present 

Androscoggin 2003 No Name Pond Lewiston Y Present 

Kennebec, Androscoggin 2004 Androscoggin Lake Wayne N Present 

Kennebec 2004 Little Cobbosseecontee Winthrop Y Present 

Kennebec 2004 Lovejoy Pond Albion Y Present 

Androscoggin 2005 Round Pond Livermore Y Present 

Sagadahoc 2005 Nequassett Lake Woolwich Y Present 

Kennebec 2006 Mosher Pond Fayette Y Present 

Kennebec 2006 Kennebec River Augusta Y Present 

Penobscot 2006 Mud Pond Old Town Y Present 

Knox 2007 North Pond Warren Y Present 

Kennebec 2008 Kennebec River Waterville Y Present 

Cumberland 2009 Androscoggin River Brunswick Y Present 

Kennebec 2000s China Lake China N Unknown 

Androscoggin 2002 The Basin Auburn N Unknown 

Sagadahoc 2003 Wat-Tuh Lake Phippsburg N Unknown 

Hancock 2005 Great Pond Great Pond N Unknown 

Hancock 2005 Green Lake Ellsworth N Unknown 

Kennebec 2006 Pattee Pond Winslow N Unknown 

York 2006 Number One Pond Sanford N Unknown 

Penobscot 2006 Stillwater River Old Town N Unknown 

Penobscot 2006 Penobscot River Howland N Unknown 

Oxford 2007 Thompson Lake Otisfield N Unknown 

Cumberland 2007 Thompson Lake Casco N Unknown 

Cumberland 2007 Crescent Lake Raymond N Unknown 

Hancock 2007 Alligator Lake T34 MD N Unknown 

Penobscot 2008 Penobscot River Greenbush N Unknown 

Penobscot 2008 Penobscot River Howland N Unknown 

Knox 2008 Chickawaukie Pond Rockland N Unknown 

PRFP Page 214

Kennebec 2008 WhittierPond Vienna N Unknown 

Knox 2008 Seven Tree Pond Union N Unknown 

Lincoln 2003 Webber Pond Bremen unknown Extirpate 

YEAR refers to the year of the first report for the water, whether confirmed or not at the time 

LAKE is water of occurrence - the file started out as lakes but has since evolved to include flowing waters 

CONFIRMED refers to confirmation by a reputable source and often with corroborating evidence, like an indisputable photo 

etc. 

STATUS can be present (confirmed by biologist, known knowledgeable source or very well documented occurrences, such as 

indisputable photos); Unknown (reported but not confirmed by a reputable source); extirpate (was known to be present but is 

now considered extirpated depending on history and removal efforts). 

Maine Case Studies 

Northern Pike in Long Pond: While the impact of northern pike on salmon 

populations in Maine has not been studied in detail, there is strong circumstantial 

evidence that they are major predators on salmon of all sizes in some lakes. Long 

Pond in Kennebec County was traditionally a principal fishery for quality sized 

landlocked salmon with the fishery maintained by stocking of hatchery fish. Northern 

pike were first confirmed in Long Pond in 1980, and presumed to have gotten there 

either through natural dispersal from connected water bodies previously introduced 

with pike, or through an illegal introduction directly into the lake. Lucas (MDIFW, 

unpublished data) showed increasing evidence of scarring (presumed to be the 

result of attacks by pike) observed on adult salmon at Long Pond in the Belgrade 

Lakes Region was correlated with declining fall trap net catches of salmon (Figure 

1). This abrupt decline may be associated with the failure of the forage base 

possibly from several failed or weak smelt recruitment years. Trends based on poor 

smelt year class have been shown on Moosehead Lake with land locked salmon and 

lake trout. Northern pike may have contributed to weakening the year class, 

however forage base is often very large and subject to stochastic events that can 

produce very large annual fluctuations. In recent years stocking of spring yearling 

salmon has been suspended at Long Pond in favor of stocking larger fall yearling 

sized salmon in an effort to reduce pike predation. Pike have also been observed in 

the small tributaries to Long Pond, and where they are present are believed to have 

impacted native brook trout populations in the tributaries (Scott Davis MDIFW, 

personal communication; see Stony Brook scetion). 

Limited food habits data are available from Maine. At Long Pond, pike fed primarily 

on smelts. Thirty-seven pike stomachs were examined in the winters of 1994 and 

1995. Eleven (50%) of the 22 stomachs that contained food items contained smelts. 

In other pike waters in Maine, where there are few if any salmonids present, white 

perch are heavily utilized as forage by northern pike. 

PRFP Page 215

Salmon catch/day 

35 

30 

25 

20 

15 

10 

5 

0 

Salmon catch/day Percent scarred 

1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 

Year 

Figure 1. Incidence of scars and trapnet catch rates of salmon on spawning 

runs at Long Pond, Kennebec County, 1988-2000. 

Northern Pike in Stony Brook: MDIFW Region B biologists surveyed Long Pond 

tributaries in Mount Vernon for the first time on August 15, 2005. Long Pond is 

actively stocked with fall yearling landlocked salmon and spring yearling brook trout. 

Stony Brook and two proximate unnamed tributaries were surveyed to document fish 

species composition and general fish habitat condition in 2005. Small sized (127- 

229 mm length range) northern pike were documented in the two streams closest to 

Long Pond, Stony Brook and an unnamed tributary to Long Pond. Water 

temperatures at all sites were adequate for coldwater species management and are 

likely used as thermal refuges by young pike and brook trout (Figure 2). 

Stony Brook continues to be monitored and is frequently surveyed by backpack 

electrofishing to assess fish community composition at various times of the year 

(Table 2). The sample site is located downstream from the crossing with Belgrade 

Road and the existing road-stream crossing culvert is impassable to upstream fish 

movement. Northern pike have been collected at all survey events in June, July, 

August and early September. Pike in Stony Brook typically range from 65 – 195 mm 

and represent young of the year (YOY), or perhaps 1+ age fish. Three wild brook 

trout (size range 142 – 164 mm) were collected during the April 2007 sampling event 

only and are presumed to have dropped down from Stony Brook’s upper reaches. 

Across all sampling events, water temperatures range from 11.0C (Sept 07) – 21.8C 

(Aug 05) and appear to maintain adequate thermal regimes throughout summer for 

coldwater species management. 

The pattern of small sized pike present in Stony Brook during the summer months is 

consistent with juvenile pike using the stream as a refuge. Stony Brook is a small 

stream with an average width of 4.5m and does not provide adequate habitat or 

water depth for larger sized pike. It is likely that Stony Brook acts as both a thermal 

refuge and as a spatial refuge for small sized northern pike from Long Pond. Pike 

PRFP Page 216 

80 

70 

60 

50 

40 

30 

20 

10 

0 

% salmon with scars

are a coldwater species and need access to cooler water habitats at all life stages. 

Hence, juvenile pike presence in Stony Brook is consistent with temporary habitat 

use as pond temperatures rise. In addition, juvenile pike have been shown to 

disperse to and temporarily inhabit areas where larger sized pike, or other fish 

predators, tend not to inhabit. Similar juvenile pike movement and habitat use 

patterns have been correlated with anti-predatory behaviors such as avoiding 

cannibalism by larger conspecifics (Craig 2008). 

2 BKT 

19.2C 

13 PIK; 5 BKT 

18.4C 

Stony Brook 

Figure 2. MDIFW Stream Survey locations for three tributaries to Long Pond. 

All sites were surveyed on August 15, 2005. Northern pike and brook trout 

abundance at time of survey for each site denoted above. 

Table 2. Stony Brook electrofishing summary information, 2005-2008. 

Date Temp Pike BKT WHS LMB PKL BND CCB GLS 

CPUE CPUE CPUE CPUE CPUE CPUE CPUE CPUE 

Aug 15, 

2005 

21.8 0.483 0.0 0.643 0.0 0.0 0.0 0.0 0.0 

Sept 12, 

2006 

13.0 0.172 0.0 0.057 0.230 0.115 0.0 0.0 0.0 

April 26, 

2007 

9.4 0.0 0.203 0.135 0.0 0.0 0.068 0.0 0.0 

June 15, 

2007 

15.8 0.857 0.0 0.095 0.0 0.095 0.0 0.476 0.0 

July 16, 

2007 

18.6 0.727 0.0 0.121 0.0 0.0 0.121 0.364 0.0 

Aug 15, 

2007 

17.5 0.273 0.0 0.091 1.457 0.091 0.091 0.182 0.0 

Sept 17, 

2007 

11.0 0.0 0.0 0.462 0.740 0.0 0.277 0.277 0.0 

PRFP Page 217 

3 PIK 

21.8C 

LONG POND

April 24, 

2008 

15.7 0.0 0.0 0.256 0.0 0.0 0.085 0.0 0.085 

Aug 20, 

2008 

16.5 0.052 0.0 0.0 0.052 0.105 0.052 0.0 0.0 

*BKT = brook trout, WHS = white sucker, LMB = largemouth bass, PKL = chain pickerel, BND = 

blacknose dace, CCB = creek chub, GLS = golden shiner 

Northern Pike in Rome Trout Brook: Rome Trout Brook is a monitoring site in 

MDIFW’s stream brook trout monitoring project and is a tributary to Great Pond in 

Belgrade. Brook trout monitoring sites are representative of ‘good’ trout habitat, 

randomly distributed throughout Maine, and are annually monitored with intensive 

fish species and aquatic habitat data collection protocols. Complete fish species 

composition, species relative abundance, and brook trout population estimates by 

size class have been annually determined since 1993 with multi-pass electrofishing 

techniques. The monitoring site on Rome Trout Brook is approximately 1.5 km from 

the confluence with Great Pond. Northern pike were confirmed in Great Pond in 

1980. One pike was captured within the survey section in 1998, 2001, and 2002. 

2001 and 2002 also correspond to years of below average precipitation and stream 

levels were subsequently quite low (Figure 3). Years 2001 and 2002 also 

correspond to years of overall lowest fish diversity (Figure 4) and YOY brook trout 

abundance (Figure 5). 

Jan 93 

Oct 93 

July 94 

April 95 

Jan 96 

Oct 96 

July 97 

April 98 

Jan 99 

Oct 99 

July 00 

April 01 

PHDI 

Jan 02 

Oct 02 

July 03 

April 04 

Jan 05 

Oct 05 

July 06 

April 07 

Jan 08 

Figure 3. Palmer Hydrological Drought Index for Maine, 1993-2009. Negative 

values denote drought conditions with values less than –4 signifying extreme 

drought. Data source: National Climatic Data Center, NOAA. 

PRFP Page 218 

Oct 08 

8 

6 

4 

2 

0 

-2 

-4 

-6

Figure 4. Total species composition for Rome Trout Brook, 1993-2007. 

200 

180 

160 

140 

120 

100 

80 

60 

40 

20 

0 

# of YOY BKT 

# of YOY BKT 

Pike presence 

1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2006 2007 

Figure 5. Abundance of Young of the Year (YOY) brook trout in Rome 

Trout Brook, 1993-2007. YOY defined as BKT total length ≤ 88 mm 

(derived from statewide estimate of BKT size at age collected from 

August – September of any given year. 2001 and 2002 were drought 

years. 

PRFP Page 219

BKT total N N 

0 50 100 150 

1993 

1994 

1995 

1996 

1997 

1998 

1999 

Pike presence 

2000 

year 

Figure 6. Total abundance of brook trout for Rome Trout Brook, 1993-2007. 

One pike 

found in monitoring site in 1998, 2001, and 2002. 2001 and 2002 were drought 

years. 

Brook trout abundance in Rome Trout Brook varies annually with the lowest 

abundance in 2001 and 2002 (Figure 6). The lowest numbers of brook trout young 

of the year also occurred in 2001 and 2002 (Figure 5). Pike presence within this 

stream is not common with only 3 total pike being detected; one each in year 1998, 

2001 and 2002. It is difficult to determine if the greatly reduced brook trout indices 

for 2001 and 2002 are the result of pike presence at the time of the survey or if low 

flow and drought conditions exacerbated the effect (Figure 3). However, in the only 

year that pike were present and water conditions were normal, brook trout 

abundance and YOY abundance were within the range of annual variation in years 

that pike were absent. Those years also show the lowest overall relative fish species 

diversity and abundance that are indicative of drought stress. It is possible that pike 

intrusion 1.5 km upstream from their source lake is not a common occurrence and is 

precipitated by environmental stress that forces some individuals to take extreme 

chances in unusual conditions. 

Baker Branch of the St John River: Muskellunge (Esox masquinongy) are an Esocid 

fish similar in morphology and ecology to northern pike. Muskellunge occur in 

Maine’s St. John River system presumably as a result of legal stocking events in 

Quebec’s Lac Frontiere in the late 1960s. Although muskellunge tend to move 

much greater distances than other esocids and tend to prefer large river habitats 

over truly lentic areas whereas pike tend to be the opposite, the fish community 

effects and habitat relationships caused by muskellunge are similar to the ecology of 

PRFP Page 220 

2001 

2002 

2003 

2004 

BKT 

2006 

2007

northern pike (Lucas 2008, Scott and Crossman 1973). Muskellunge presence was 

confirmed in Baker Lake in 1986 and Yoder’s survey of the St. John River found 

muskellunge presence in ten of fourteen surveyed reaches (2005). 

MDIFW conducted raft electrofishing surveys on four reaches of the Baker Branch of 

the St. John River on August 12 – 13, 2008 (Figure 7). Three surveyed reaches 

were above the confluence with Baker Lake and one reach was below the lake. 

Figure 7 Raft electrofishing surveys on four reaches of the Baker Branch of 

the St. John River on August 12 – 13, 2008. 

PRFP Page 221

Muskellunge in the Baker Branch of the St. John River were caught in the three 

reaches in closest proximity to Baker Lake. The reach furthest from Baker Lake, 

ABOVE1, had no muskellunge caught, the highest catch rate of soft rayed fish 

species (Figure 8) and the greatest overall species richness (Table 3). This pattern 

may be a reflection of ecological displacement where the presence of muskellunge 

shifts the fish community toward less preferred prey species. Muskellunge, like 

northern pike, prefer soft-rayed fish species as forage when choices occur. Fishes 

do vacate habitats or areas where predators are known to occur or are detected (He 

and Kitchell 1990). Ecological displacement supports the pattern of a greater 

number of soft rayed fishes in the reach furthest from areas with muskellunge, as 

well as the expanded spatial pattern of brook trout presence in tributaries to the 

Baker Branch of the St. John River, but apparently not present in the mainstem 

although summer water temperatures appear to be adequate for salmonids (Figure 8 

and Table 3) and they likely occurred there historically. 

CPUE 

0.12 

0.1 

0.08 

0.06 

0.04 

0.02 

0 

Muskie CPUE 

Soft ray CPUE 

Yellow Perch CPUE 

Below Above3 Above2 Above1 

Figure 8. Catch per electrofishing second for surveyed reaches of the Baker Branch of the St. 

John River, August 2008. Soft ray CPUE is catch per effort for fallfish, white sucker, golden 

shiner, common shiner, burbot, blacknose dace, and creek chub combined. 

Table 3 Summarized results for four surveyed reaches of the Baker Branch of the St. John River, August 12-13, 2008. 

Reach Habitat Type Temp C Electrofishing Species Species* 

time (sec) Richness 

Below Rapid 18.2 548 4 MUS, FLF, 

YLP, WHS, 

Above3 Deadwater 17.7 559 4 MUS, FLF, 

YLP, GLS 

Above2 Run 16.7 558 4 MUS, YLP, 

WHS, CMS 

PRFP Page 222

Above1 Run 16.3 551 7 FLF, YLP, 

WHS, CSK, 

BND, CCB, 

CMS 

* MUS = Muskellunge, FLF = Fallfish, YLP= Yellow Perch, WHS = White Sucker, GLS = Golden 

Shiner, CMS = Common Shiner, CSK = Burbot/Cusk, BND = Blacknose Dace, CCB = Creek Chub 

Chain pickerel: A study conducted by MDIFW in the 1960s revealed that pickerel 

were the most common predator on newly stocked salmon. Predation by pickerel 

was observed at 27 of 42 lakes (64%) shortly after stocking of landlocked salmon 

(Warner 1972). In all, 152 of 523 pickerel examined (30%) were found to have 

recently consumed a newly stocked salmon. The average number of salmon per 

pickerel was 1.9 fish; however one fish devoured 32 newly stocked salmon. 

Barr (1962) reported significant predation on migrating sea-run Atlantic salmon 

smolts by pickerel at Beddington Lake in the Narraguagus River drainage. In that 

study, 21% of pickerel greater than 10 inches long were found to have consumed a 

salmon smolt. Similarly, on the Penobscot River, Van den Ende (1993) documented 

that Atlantic salmon smolts were the most important dietary item of chain pickerel 

(11.5 - 24 inches in length) during the smolt run period on the Penobscot River, 

where 58 percent of all pickerel stomachs contained food items and smolts 

represented 80 percent of the wet weight of all prey items. 

Pickerel predation on newly stocked brown trout was observed at Brandy Pond in 

Hancock County in 1989. In that study, newly stocked spring yearling brown trout 

were observed in the stomachs of 15 of 54 pickerel (28%). The smallest pickerel 

that consumed a brown trout was 15 inches long. The mean length of the 54 

pickerel examined was 16.9 inches. The experimental stocking was terminated due 

to unsatisfactory survival. 

Changes to Fish Communities after Introductions 

Invasions or introductions of top predators into new ecosystems have been shown to 

have negative effects on native top predators and dramatic cascading effects on 

lower trophic levels (Vander Zanden et al. 2004). Several studies have attributed 

large losses of stocked and migrating salmonids to pike predation in riverine 

ecosystems. Petrvozvanskiy et al. (1988) documented that pike account for 

approximately 35% of stocked Atlantic salmon smolt mortality in the Keret River in 

Russia. Similarly, Larson (1985) and Kekäläinen (2008) attributed a 50% and 29% 

loss respectively of migrating juvenile Baltic salmon to predation from pike. Jepsen 

et al. (2006), working with hatchery stocked Atlantic salmon smolts and wild brown 

trout observed 56% predation by pike during spring migration through Lake Tange, a 

12 kilometer long reservoir in the Danish River Gudenå watershed. Rutz 

(1996,1999) documented that juvenile salmon and trout species were the preferred 

forage of pike in several southcentral Alaskan waters. Rutz reported that 80% of the 

non-empty pike stomachs from the Susitna River contained salmonids, even though 

suckers, sticklebacks, and other minnow species were present. He also notes that 

many of Susitna drainage lakes and streams that once contained native populations 

PRFP Page 223

of coho, chinook and sockeye salmon, rainbow trout, and Arctic grayling now contain 

only northern pike. 

Studies in lake ecosystems have shown negative effects on the native top predators. 

In Sweden, northern pike replaced artic char (Salvelinus alpinus) as top predator 

after invasion by a combination of predation and competition (Bystrom et al. 2007). 

The study also reported a possible extinction of char and increases in zooplankton 

and benthos. He and Kitchell (1990) documented changes after an experimental 

northern pike introduction into a lake that was previously piscivore free. Changes 

occurring in the fish community after northern pike introduction ranged from 

decreased prey fish biomass, decreased abundance of dominant species and 

decreased mean size for species most vulnerable to predation (He and Kitchell 

1990). In a similar experiment, Findlay et al. (2005) reported that a non-native 

northern pike introduction into a small boreal lake resulted in one native species 

(Semotilus magariscus) was extirpated and another native species (Perca 

flavescens) declined in abundance. 

Native Species Habitat and Diet Preferences 

Brook Trout -Stream populations: It has been well documented that brook trout 

prefer cool water. Baldwin (1956) reported that optimum growth rates occurred 

around 16.5 o C. Bonney (2006) reports the upper lethal temperature limit for brook 

trout at 25 o C. Resident stream populations of wild/native brook trout will spawn in 

shallow gravel areas of headwater streams. The spawning material may vary from 

fine sand to coarse, loose gravel and rubble (Everhart 1976). Brook trout prefer 

substrates that also are influenced with spring upwellings. Young of the year brook 

trout are typically located in shallow gravel riffle areas of these streams throughout 

the summer months and in areas around springs. Griffith (1972) reports that streamdwelling 

juvenile brook trout prefer low water velocities (0.03 to 0.08 feet/second). 

As stream resident brook trout reach older ages, they tend to prefer deeper habitats. 

Bonney (2006) notes that adult fish tend to migrate to pools in late summer and late 

winter and that pool habitat is critical to brook trout survival in periods of low water 

and high water temperature. MacMillian (1998) also reports that predator marks 

increased in frequency on brook trout crowded into pools during periods of warm 

temperatures. 

Brook Trout - Lake populations: Brook trout inhabit ponds and lakes in Maine with a 

wide range of physical and biological characteristics. The vast majority of remaining 

wild and native populations are located in the northern and western regions of the 

state. Brook trout were distributed over the entire state prior to European settlement. 

Since this time, habitat degradation associated with development and the 

introduction of exotic species has greatly diminished the range of wild/native brook 

trout in southern and eastern Maine. Most of the brook trout fisheries in these 

impacted areas are supported entirely by stocking programs. 

Brook trout in lakes and ponds typically inhabit littoral habitat during most times of 

the year. Brook trout abundance is often related to the amount of littoral habitat in 

PRFP Page 224

any given water. During warmer periods of the summer when water temperatures 

are highest, brook trout may seek deeper water refuge but are not commonly found 

in depths exceeding 9m. A recent year long radio telemetry study of brook trout in 

Chamberlain Lake confirmed that during the winter months the majority of tagged 

brook trout were in shallow bays with maximum depths less than 6m. These fish 

stayed in these shallow locations for the duration of the winter. Tagged brook trout 

moved freely around the 13,000-acre oligotrophic lake system during the spring, but 

were usually located in littoral habitat near the shoreline. 

Brook trout in large lakes typically spawn in tributaries. Spawning runs are often 

influenced by weather conditions, primarily rain events, but usually begin in early 

September in northern Maine. Actual spawning typically occurs from mid-October 

through early November in Maine. Lake-dwelling brook trout seek the same type of 

spawning substrate as stream-dwelling brook trout. Brook trout will travel several 

miles upstream in tributaries to locate suitable spawning habitat. Brook trout in small 

ponds often spawn along the shore in areas where there is a spring influence when 

tributaries are not present. Auclair (1982) found that wild brook trout fry dropped out 

of their natal streams soon after hatching. 

Food habits of brook trout are very flexible. Bonney (2006) summarized data 

collected from the examination of over 1,700 brook trout stomachs in the 

Moosehead Lake Region. Insects occurred in 50% of all stomachs examined, 

accounting for 34% of the total volume of food. Unidentified fish remains, smelts, 

and crayfish were also important food items for brook trout sampled from a variety of 

waters. 

Landlocked Salmon: Naturally produced landlocked salmon populations have two 

distinct life phases: stream life and lake life. After hatching in the spring, young wild 

salmon live in their natal stream for one to three years. Salmon move into lake 

habitat after smoltification occurs. In Maine, there are a handful of rivers that have 

year-round salmon populations. One of the largest and most important river fisheries 

for wild landlocked salmon is the West Branch of the Penobscot River between 

Ripogenus Dam and Pemadumcook Lake. 

Spawning occurs in gravel substrate in flowing water. Salmon move into streams 

and rivers in September and October, while the actual act of spawning generally 

occurs in late October through the month of November. The young salmon emerge 

from the redds in late April or early May. Young of the year salmon prefer shallow 

gravel habitat for the first summer. Salmon parr (stream life fish greater than age 

one) can withstand higher water velocities and are typically found in rocky riffle/run 

habitat. As the salmon matures, parr marks become less apparent and it undergoes 

smoltification process similar to Atlantic salmon, but less pronounced. It is during 

this time that the salmon migrate to lake habitat. Most movement out of the natal 

stream occurs in the spring (Warner and Harvey 1985). 

PRFP Page 225

Adult landlocked salmon, both wild and hatchery origin, can occur in a wide range of 

lake types including: oligotrophic, mesotrophic, and even a few homothermous 

waters. Salmon prefer cool, well oxygenated water but can exist in less favorable 

conditions. Adult salmon are generally located in the thermocline in the summer 

months if stratification occurs. They can frequently be found in the pelagic areas of 

these lakes. In the winter months, salmon are found not only suspended over 

deeper areas, but also in the littoral areas of lakes. Location of forage fish, primarily 

smelts, will often dictate the location of adult salmon. In the West Branch of the 

Penobscot River, adult salmon overwinter in large deadwaters in the lower reaches 

of the river. Spear (in FERC Project No 2572, 1991) found that the most important 

overwintering deadwaters contained low velocities, shallow bays and logans, and 

muddy substrate. 

Food habits of YOY salmon were examined during the relicensing of the Ripogenus 

Dam in Maine. Data collected by Great Northern Paper Co., Inc were presented in 

Warner and Harvey (1985). These young salmon were feeding primarily on insects 

including Ephemeroptera , Diptera, and Tricoptera. There is a paucity of information 

of the food habits of salmon parr although it is likely they feed similarly on insects. 

Adult landlocked salmon also feed on aquatic insects during summer months. 

However, smelts are considered the primary food source for adult salmon. Warner 

and Harvey (1985) details the importance of smelts for salmon growth and survival. 

Smelt populations are notorious for wide fluctuations in density, which frequently 

results in poor growth for salmonids. Alternative food sources, such as landlocked 

alewives, have been established in some salmon waters. In Echo Lake, smelt 

growth suffered after the introduction of landlocked alewives (Warner and Harvey 

1985). Many of Maine’s tailwater river fisheries for landlocked salmon also benefit 

from smelt drift from impoundments upstream, which helps to sustain salmon growth 

in the river population. Spear (in FERC Project No 2572, 1991) estimated the 

average total annual discharge of smelts into the West Branch of the Penobscot 

River through the Ripogenus Dam from 1985 to 1989 to be 27,683 lbs. This section 

of river is managed for trophy landlocked salmon. 

Lake trout: Lake trout thrive in oligotrophic lakes. In the summer months they are 

typically found in the hypolimnion and they prefer temperatures around 10 o C (Scott 

and Crossman 1973). In the winter they can be found at any depth. During the 

spring months, before stratification occurs, lake trout are often found in the littoral 

zone. They can be occasionally found in larger tributaries to lakes in the spring, 

especially during periods when smelts are spawning. In Maine, young lake trout are 

found in the deepest basins (> 30m) during the summer months. Lake trout spawn 

on rocky shoals and shorelines in mid to late October in Maine. The eggs are 

scattered amongst the rocks and settle in the crevices, where they overwinter. 

Water depth over egg deposition may vary, but Auclair (1985) states that lake trout 

eggs were deposited in approximately one meter of water on shoals in Moosehead 

Lake. Subsequent work on Moosehead Lake supports Auclair’s findings. 

PRFP Page 226

In Maine, lake trout feed primarily on smelts. From 1985 to 2006, MDIFW staff 

examined 593 lake trout stomachs from Sebec Lake. Smelts occurred in 61% of the 

stomachs containing food and constituted 51% of the total volume of food items. 

White perch were the next most important identifiable prey item occurring in 26% of 

the stomachs with food and representing 26% of the total volume. From 1971-2006, 

3,267 lake trout stomachs were examined from Moosehead Lake. Smelts were by 

far the most important food item. Smelts occurred in 72% of the stomachs containing 

food and represented 81% of the total volume of food. The next most important food 

item was yellow perch, which occurred in just 4% of the stomachs containing food, 

and represented 4 % of the total volume. Of the 20 other identified fish or 

invertebrate food items in the sample, none exceeded 3% of the total volume. 

Atlantic Salmon: Danie et al. (1984) provides the following summary of salmon life 

history. Atlantic salmon ascend freshwater streams to spawn on gravel substrate 

from mid-October to mid-November. In Maine, eggs incubate for 175 to 195 days 

depending on water temperature, and hatch in April or early May. After hatching, the 

15 mm long yolk-sac larvae (alevins) remain buried in the gravel depressions for up 

to six weeks while absorbing the yolk-sac for nourishment. The resulting 25 mm long 

fry begin foraging for themselves and emerge, usually at night, from the gravel 

depressions. Larger freshwater juveniles (parr) will remain in riffle sections of 

streams until they are 125-150 mm in length, which may take from two to three 

years. Failure to attain this length by spring or early summer of the year will prevent 

parr from transforming into smolts (seaward migrating juveniles). After attaining this 

critical length, parr undergo smoltification, which includes physical and physiological 

changes adaptive to a migration to a marine environment. The parr marks disappear 

and the skin develops a silvery pigmentation from deposition of guanine in the skin, 

the tail lengthens and becomes more deeply forked, and schooling behavior 

develops. Increases in water temperature and water level trigger downstream 

migration of smolts. Smolts from the western Atlantic migrate, within 3m of the 

surface of the ocean, to feeding areas in the Davis Strait between Labrador and 

Greenland. Atlantic salmon will return to natal rivers to spawn after one (grilse) or 

two (bright salmon) years at sea. Salmon accumulate in estuaries, bays, and river 

mouths, before ascending streams. Upstream migration of salmon coincides with 

increases in water flow. Adult salmon do not feed while in freshwater. Atlantic 

salmon do not consistently die after spawning, and many spent fish (kelts) survive 

the winter in freshwater and begin to feed again. Mortality is high when kelts enter 

saltwater. Those kelts that survive and migrate to feeding grounds in the Davis 

Strait, may become repeat spawners. (From USFWS 

(http://www.fws.gov/r5gomp/gom/habitatstudy/metadata/Atlantic_salmon_model.htm). 

Risks to Native Species from Niche Overlap 

Habitat in the mainstem of the Piscataquis River and the Sebec River are likely both 

suitable for the establishment of resident pike populations (Figure 10). Both rivers 

are stocked with spring and fall yearling brook trout. These fish are scattered 

throughout the Piscataquis River from Abbot to East Dover, including into or near 

many deadwater areas that would likely hold adult and sub-adult pike if they are 

there. The Sebec River is stocked below the Sebec Lake Dam into run/pool habitat, 

PRFP Page 227

and in the Town of Milo below the Milo Dam deadwater. Pike are known to prefer 

soft-rayed fish as forage (Petrvozvanskiy 1988; Hakanson 2002), including stocked 

salmonids, and therefore, it is likely that there will be impacts on the stocked brook 

trout fisheries in these river systems. 

Current barriers on the Sebec River prohibit pike passage into the section below the 

Sebec Dam, however, brook trout stocked below the Milo Dam may be vulnerable to 

predation from northern pike. There are dams on the mainstem of the Piscataquis 

located in the Towns of Dover-Foxcroft and Guilford, which could potentially pass 

pike via existing fishways. A barrier to pike in the existing fishway at the Browns Mill 

Project in South Dover would protect approximately 80% of the stocked area from 

the establishment of pike through natural dispersal. 

The mainstem of the Pleasant River in Brownville is also stocked with spring yearling 

brook trout and there are no barriers to prevent the natural movement of northern 

pike into this section of river. There are deadwater areas in this section that 

contribute to the trout fishery. Pike could impact the stocked fishery in this area 

through direct predation on stocked brook trout. 

There are natural barriers at Gauntlet Falls and Gulf Hagas on the East and West 

Branches of the Pleasant River. However, there are large areas that contain intact 

wild brook trout populations below these impasses and there are no alternatives for 

prohibiting natural pike dispersal from these areas. These rivers are unlikely to hold 

large populations of adult pike due to unsuitable pike habitat. However, Silver Lake, 

Upper Ebeemee Lake, and Lower Ebeemee Lake are suitable pike habitat and are 

located within these systems. There are also areas suitable for pike interspersed in 

several wild trout streams including: Rapid Brook, Whetstone Brook, Roaring Brook, 

and Houston Brook. 

There are numerous small streams in the Piscataquis River drainage. While only a 

small percentage have been inventoried, it is likely that many, if not most, of the 

small streams that have a source of coldwater will also contain resident populations 

of wild brook trout. Young pike have been documented in these types of habitats in 

Maine during summer months in streams that are within close proximity to lakes with 

self-sustaining pike populations. Since young pike do occasionally occur in these 

habitats and they prefer soft-rayed fish there could be impacts at the local level for 

these wild trout populations, through direct predation or competition for thermal 

refuge. 

As previously stated, it is possible to create a barrier on the mainstem of the 

Piscataquis River, which would protect some of these streams. However, many 

more exist in areas where there are no large-scale opportunities to preclude pike 

movement. Therefore, in these areas, each small tributary will have to be 

individually assessed for opportunities to create pike barriers, such as altering 

culverts. Recent stream crossing assessments by the Maine Forest Service for the 

PRFP Page 228

Piscataquis drainage will likely offer opportunities to identify specific road-stream 

crossings for restricting pike passage into quality brook trout streams. 

There is considerable niche overlap between northern pike and brook trout in 

lacustrine habitat. Both prefer the littoral zone and both may seek cool water during 

the warmest periods of the summer. In winter months, brook trout are almost 

exclusively found in shallow areas of lakes and ponds. Radio telemetry data from 

Pushaw Lake indicate that pike may be found in the deeper areas of the lake during 

the winter months, yet most anglers fish for pike in depths less than 7m during the 

ice fishing season. Direct predation is possible in situations where pike and brook 

trout occupy the same areas, as well as competition for forage, such as minnow 

species and rainbow smelts. 

Most of the wild/native brook trout lakes in this drainage are already protected from 

pike due to natural barriers. There are two wild/native brook trout ponds that are not 

protected by such a barrier. Both of these ponds are small and relatively shallow. 

Dow Pond is classified as a wild brook trout water. It has a principal fishery for brook 

trout and has not been stocked in over 25 years. Greenleaf Pond in Abbot also 

contains a principal fishery for brook trout and has never been stocked. The 

stocking status was unclear at the time of the last IFW inventory update, but a 

subsequent review of the historical stocking archives failed to produce any record of 

stocking and a follow-up field survey is scheduled for 2009. This pond also contains 

pickerel and, therefore, it is likely that pike would have access to this water if they 

were able to reach the outlet that flows into the Piscataquis River in Abbot. 

The outlet to Dow Pond is below the Brown’s Mill Dam and therefore, any pike 

barrier on the mainstem of the Piscataquis River would not affect passage to this 

wild trout pond. Currently there are no pickerel in Dow Pond, which suggests that a 

culvert on the Rtes 6 and 16 crossing is effectively preventing pickerel from 

accessing Dow Pond. 

The outlet of Greenleaf Pond is above the Guilford Dam, therefore a barrier on the 

mainstem below Guilford could eliminate the risk from the establishment of pike 

through natural dispersal. 

There are many waters in the Piscataquis Drainage that have coldwater fisheries 

maintained through stocking. Many are upstream of natural barriers. There are 

several stocked brook trout and splake waters in the Piscataquis Drainage not 

protected by natural barriers including such as Cedar Lake and Endless Lake. 

Impacts on these stocked fisheries are likely to be more severe at Endless Lake due 

to the available pike habitat. Schoodic Lake and Seboeis Lake are both stocked with 

brook trout and/or splake. There are no natural barriers to these waters, although 

existing dams currently prohibit the movement of pike into these lakes. 

The potential for northern pike to adversely impact landlocked salmon populations is 

higher in lakes than in rivers and streams primarily because of the differing habitat 

PRFP Page 229

equirements between the two species. Predation of salmon by pike could be a 

factor at habitat edges, for example at points where riffle tail waters into a pool or 

dead water section of stream. Foraging competition would likely be insignificant 

where juvenile pike and salmon populations to exist in close proximity to one 

another. 

Juvenile salmon migrate from streams to lakes at age 1 to 3 years old 

(smoltification) and may be vulnerable to predation by adult pike if the migration 

route involves long stretches of dead water suitable for adult pike. Likewise, juvenile 

salmon will be vulnerable to predation by pike in the lake until they reach an 

adequate size to escape being eaten. However, even adult salmon in Long Pond, 

Maine have been observed to have scars presumed to be from Northern pike. 

Competition for forage may exist between salmon and pike in lakes, particularly if 

forage is limited resulting in a situation where both species are relying heavily upon 

rainbow smelt. 

The impact of Northern pike on populations of lake trout (togue) will likely be low, as 

togue thrive in oligotrophic lakes and Northern pike tend to do better in mesotrophic 

lakes. Adverse interactions between juvenile life stages of the two species, either 

through competition for resources or through predation is low, as lake trout utilize 

deeper areas of lakes beginning at a very young age, while young pike prefer 

shallow vegetated waters. Likewise, adult lake trout prefer much deeper water 

depth’s than pike during the summer, so little interaction would be expected during 

that time of year. Pike may compete with lake trout for forage. As with salmon, lake 

trout prefer smelt when available, and may grow poorly if smelt are limited supply. 

Lake trout are a slow growing; therefore they may be vulnerable to predation for a 

longer time period than other salmonids. 

At the youngest juvenile life stages of Atlantic salmon and northern pike, there is no 

evidence for potential habitat overlap. Both species require very specialized habitats 

for growth and survival. Juvenile pike generally require “increase of water depth by 

approximately 10cm deep for every week after peak spawning, until fish reach 

150mm in length” (Casselman, 1995), which tends to be the opposite of salmon and 

will further distinguish habitat preferences. 

During the smolt stage, pike may pose the greatest threat. At this time, all young of 

year (YOY) pike (>150mm) as well as sub-adults have reached a size where the 

average smolt size is within the prey size range for pike (Hart and Hamrin 1988, 

Nilsson and Brönmark 1999, Vehanen 2004). With the onset of spring, longer days 

and warmer waters stimulate mature pike to congregate near river and stream inlets 

in preparation for spawning. At this time, salmon smolts may be at the greatest risk, 

since they are going through physiological changes preparing them for a down river 

migration through many varying habitats. In these river corridors, waters have 

typically reached temperatures above 9°C (Casselman , 1978) where increases in 

juvenile NP swimming activity occur; temperatures less than this and below 6°C 

show less sign of swimming activity. Adult NP show “rapid somatic growth at 

PRFP Page 230

approximately 14°C”. These temperatures, 9-14°C ar e ideal for migrating salmon 

smolts, and raises increased concern for the predation of smolt during migration. If 

an Atlantic salmon population exists all migrating smolts may pass through areas 

where pike have congregated. As pike dispersal tends to occur in a downstream 

manner (Casselman, conference call March 13, 2009), this perpetuates the risk of 

pike predation on smolts as new pike populations become established throughout 

the down stream salmon migration corridor. This could also be the case if pike 

populations established themselves up a river system, which has been the case in 

Alaskan rivers and streams (Dave Rutz, Alaska Department of Fish and Game 

Division of Sport Fish, e-mail conversation with Tim Obrey, Regional Fisheries 

Biologist Moosehead Lake Region Maine Inland Fisheries and Wildlife, March 20, 

2009). 

Returning adult salmon have presumably reached a size, which in general has 

excluded them from being prey for juvenile and sub-adult pike. If a substantial pike 

population persists, larger adult pike could pose a threat to one sea winter and some 

two-sea winter adult salmon, in estuaries, head ponds and bogin areas leading to 

summer thermal refugia or spawning shoals. This migration may pose a threat to 

returning salmon when larger pike are seeking food sources. 

Potential Habitat Model for Northern Pike 

General 

Northern pike are distributed throughout much of the northern hemisphere, including 

North America and Eurasia (Brautigam 2001). They are not native in Maine or the 

rest of New England except in Lake Champlain in western Vermont. 

Northern pike can tolerate a wide range of environmental conditions but are primarily 

a cool-water species best adapted to shallow (< 12 m), productive, mesotrophiceutrophic 

environments (Brautigam 2001; Casselman and Lewis 1996). Pike 

generally become well established in habitats that are relatively shallow and contain 

abundant emergent wetland and submerged aquatic vegetation, which is needed for 

spawning, nursery and for juvenile and adult foraging habitat. Pike can occur in 

oligotrophic waters, but more commonly inhabit mesotrophic or borderline eutrophic 

lakes and ponds (Inskip 1982). They are known to tolerate brackish water 

conditions (salinities less than 7 ppt). 

Northern pike show age-based and seasonal shifts in habitat. As northern pike 

mature, their vegetation preference changes from emergent wetland for fry to 

emergent wetland and aquatic macrophytes (submerged and floating) for juveniles 

to submerged aquatic vegetation for adults (Casselman and Lewis 1996). They 

typically occur in shallow water in the spring and fall, and seek relatively deeper 

water during the height of the summer and in winter in response to environmental 

conditions. During the summer, northern pike will seek cooler temperatures when 

water temperature exceeds 20°C and are physiologica l impacted (lose of weight) at 

surface temperature above 25°C (Casselman and Lewis 1996). In winter, northern 

PRFP Page 231

pike tend to occupy deeper habitats in response to ice cover, die-back of vegetation 

and oxygen depletion (Casselman and Lewis 1996). 

Spawning Habitat 

Northern pike spawn in shallow, sheltered water over vegetation in spring shortly 

after ice-out, when these shallows have warmed to 8-12°C (Casselman and Lewis 

1996; Brautigam 2001). Emergent wetland, such as grasses and sedges, are 

preferred spawning substrates, but other vegetation may also be used but would be 

considered poorer quality spawning habitat (Casselman and Lewis 1996). 

Adult pike will migrate certain distances to spawning habitat (Inskip 1982). In 

general, pike do not disperse widely and utilize the nearest suitable spawning site 

(Craig 2008). Evidence for both spawning-site and natal-site fidelity has been 

shown by mark and recapture experiments and by population genetics, which 

support previous findings (Craig 2008; Inskip 1982). The absence of inundated 

vegetation can inhibit spawning, and spawning success is strongly influenced by 

water-level changes (Inskip 1982). High water levels at time of spawning with 

stable levels after incubation period are optimum (Caselman and Lewis 1996). 

Caselman and Lewis (1996) developed a qualitative rating for spawning habitat and 

identified several factors that were essential for spawning habitat, including 

vegetation type and density, water level depth, water fluctuation and the exposure of 

the location. 

Nursery Habitat 

In the early life stages, northern pike are highly dependent on vegetation and their 

behavior and survival may depend on the extent and form of cover (Craig 2008). 

Casselman and Lewis (1996) identified three optimum criteria for nursery habitat. 

The best habitat is contiguous with the spawning habitat; is composed of dense 

emergent wetland or aquatic macrophytes with between 40 and 90% cover; and is 

greater than 10 times the area of spawning habitat. 

The habitat frequented by young northern pike during the first year is described by 

an increase of water depth by approximately 10 cm deep for every week after peak 

spawning, until the fish reach 150 mm in length (Casselman and Lewis 1996). The 

deepest depth occupied by young-of-year northern pike was about 250 cm. 

Temperature is a very important factor for young-of-year northern pike. The 

optimum temperature range is 22 to 23°C, a higher o ptimal temperature than 

juvenile or adult fish. Casselman and Lewis (1996) also found a significant 

correlation between year-class strength and mean temperature for July and August 

where either a lower or higher temperature deviation from optimum resulted in much 

reduced year-class strength. 

Juvenile and Adult Habitat 

Juvenile and adult northern pike are visual predators and are primarily active during 

the day but usually feed crepuscularly. Their “ambush” predation style requires 

PRFP Page 232

cover, and aquatic macrophytes are preferred (Craig 2008). Adult northern pike are 

generally found near the edge of vegetation or are otherwise associated with 

structure in the lake and are typically sedentary (Brautigam 2001). A water body 

typically needs more than 25 % submerged macrophytes for a northern pike 

dominated fish community to exist (Casselman and Lewis 1996). Optimal conditions 

for juvenile and adult habitat occur with intermediate densities of vegetative cover. 

Catches of juvenile and adult northern pike were low at low macrophyte densities, 

highest at intermediate densities (35%-80%) and low in very dense, continuous 

vegetation (Casselman and Lewis 1996). 

Although northern pike generally prefer shallow vegetated areas (usually less than 4 

m but sometimes as deep as 12 m) they are not necessarily strongly tied to this 

habitat and exhibit some versatility in habitat selection. The selection and use of 

vegetated areas depends on the size of fish with larger fish observed at the 

vegetated, open-water, or at the interface of these habitats and the smaller fish 

selecting more heavily vegetated areas (Casselman and Lewis 1996). 

Temperature is an important environmental factor for northern pike with optimal 

temperature being 19 to 21°C (Casselman and Lewis 1 996). Northern pike seek 

cooler temperatures when water temperature exceeds 20°C; are physiologically 

impacted (loss of weight) at surface temperatures above 25°C; and are significantly 

(even lethally) impaired above a range of 29.4 and 30°C (Casselman and Lewis 

1996). Early summer temperatures below 18°C are su boptimal for adult pike and 

will not result in the establishment of resident populations (J. Casselman, Queen’s 

University, personal communication, February 11, 2009). This relatively narrow 

water temperature tolerance may explain why northern pike typically retreat to 

deeper, colder areas in summer, yet northern pike rarely occur below the 

thermocline in lakes that stratify (Inskip 1982). 

Northern pike are relatively tolerant of low dissolved oxygen, but can be impacted by 

anoxic conditions either in summer or winter (Inskip 1982). Well-oxygenated water 

in spawning and adjacent nursery habitat appears to be important for optimal 

reproduction of northern pike (Casselman and Lewis 1996). 

Northern pike have been found to be flexible in their response to water clarity and 

difference in behavior can be found within locations and populations (Craig 2008). 

Casselman and Lewis (1996) found that northern pike weight was positively related 

to Secchi depth. For Secchi depth over 3 meters then an increase in Secchi depth 

of 1 meter resulted in an increase in northern pike weight of 6 percent. 

Northern pike are not adapted to strong currents. Riverine habitat may be suitable 

for pike if it resembles a lake environment, i.e., standing or very slow moving. Water 

velocity exceeding 1.5 m/s can block spawning migrations (Inskip 1982). Northern 

pike have little use for riverine habitats where the gradient exceeds 5 m/km (0.5 % 

slope), and have less tolerance for gradient than muskellunge (Inskip 1982). 

PRFP Page 233

However, it was determined that northern pike dispersal in Sweden was precluded 

only when maximum stream slope approached 6.6 % (Spens et al. 2007). 

Dispersal 

Emigration and immigration can play an important role in fish population dynamics, 

however dispersal does not appear to be a significant population mechanism for the 

northern pike (Craig 2008). They are mainly but not exclusively sedentary and do 

not move far from a home range (Craig 2008). Northern pike that disperse or 

migrate exhibit homing behavior as they generally returned to the same spawning 

area the following year (Craig 2008). Females rather than males generally move 

greater distances (Koed et al. 2006). However, the migration distances between 

summer and spawning habitat are typically less than 2 kilometer and not more than 

10 kilometers (J. Casselman, Queen’s University, personal communication, 

February 11, 2009). 

Potential Habitat Model 

Abiotic factors, such as temperature and vegetation, on northern pike population 

dynamics are well established (Craig 2008). Several of these factors were used to 

develop a model of potential habitat for pike in the Piscataquis River watershed. A 

model is a representation of a system or process that can be used to define a 

problem, organize an approach, understand the available data and make predictions 

(Starfield and Bleloch1986). Given that models are representations, they have 

limitations based on the level of understanding one has about the issue and the type 

of data that is available. 

For northern pike, the scientific literature is well established and provides a robust 

level of understanding. However, data on northern pike (and to some extent our 

understanding) in Maine is limited. A model is one way to support management 

decisions that will be made on the overall risk from northern pike when there is 

uncertainty in our understanding or available data. The modeling approached was 

based on examining the critical habitat criteria for northern pike discussed above, 

developing indicators from the literature for representing the habitat criteria and then 

applying the indicators to develop a combined measure of habitat potential. 

Two potential habitat models were developed based on waterbodies (lakes and 

ponds) and waterways (streams and rivers). The models are based on the factors 

and measures that could be developed using existing information for the watershed 

(Tables 4 and 5). The model results are representative of habitat conditions based 

on the best available information and assume a positive relationship between habitat 

conditions and the capacity for establishing resident pike populations. The results 

are provided as a ranking (low, medium or high potential) for waterbodies and as a 

value of 0 to 1 (0 being no or low suitability) for waterways. 

Methods 

Tables 4 and 5 describe the measures that were developed as critical habitat 

parameters based on: 1) the literature on the habitat requirements of northern pike 

PRFP Page 234

and 2) the availability of data in Maine available for the watershed. The habitat 

parameters were developed first and then applied without prior knowledge or 

through the direct use of the waterbody/waterway characteristics. Morphometric 

characteristics and water quality data were obtained from MDIFW (M. Gallagher, 

Fisheries Research Station, Bangor) and MDEP (R. Bouchard, Lake Monitoring 

Program, Augusta). Wetland coverage and type were obtained through the National 

Wetland Inventory. Waterway data was obtained by modifying a model developed to 

predict Atlantic salmon spawning and rearing habitat in Maine (Wright et al. 2008) 

through the use of hydraulic-geometry relations developed by Dudley (2004) for 

rivers in coastal and central Maine. 

The waterbody classification was completed for 196 lakes and ponds in the 

Piscataquis River watershed and was limited to those waterbodies that were greater 

than 2 HA (about 5 acres). Not all parameters were used in the waterbody 

classification because of the lack of water quality data. Early summer temperature 

(parameter 8) was available for only two lakes, total nitrogen (parameter 6) was 

available for 5 lakes, and summer water temperature was available for 26 lakes. 

These parameters were not used in the ranking approach. The lack of temperature 

data was unfortunate since Casselman and Lewis (1996) found that temperature 

was a significant parameter for determining the potential to develop a resident 

population. 

The waterbody model used a variation of the simple multiple attribute ranking 

technique (Goodwin and Wright 2004). Each waterbody was classified into low, 

medium and high categories for each of the six parameters (Table 4). A parameter 

was not developed for a waterbody if no data was available. For example, the lake 

trophic state parameter was developed for 108 waterbodies but not for 86 

waterbodies (Table 4). A weight from 1 (less important) to 3 (more important) was 

assigned to each parameter through professional judgment of the work group to 

emphasize the importance of the life stage 

PRFP Page 235

Table 4 Northern Pike Waterbody Habitat Parameters 

No. Habitat Parameter 

1 Lake Trophic State 

2 Lake Maximum 

Depth 

3 Spawning Habitat - 

Emergent Wetland 

4 Nursery Habitat – 

Emergent Habitat 

5 1 Water Temperature 

– Year Class 

Strength Condition 

6 1 Productivity using 

Length at Age II 

7 Productivity using 

Water Clarity 

8 1 Water Temperature 

- Resident 

9 Submerged 

Vegetation – Lake 

Cover 

Low Medium High Weight No. of Waterbodies 

with Data to Apply 

Parameter 

Description 

Oligatrophic Eutrophic Mesatrophic 2 108 Lake trophic classification 

< 1 m >12 m 1 - 12 m 2 91 Preferred water depth based on macrophyte 

occurrence, water clarity and occurrence from 

PRFP Page 236 

(Casselman and Lewis 1996) 

0.15 3 196 Ratio of emergent wetland (as defined by the National 

Wetland Inventory) within 200 m of the waterbody 

shoreline to total lake area from Inskip (1982) 

7.5 3 196 Northern pike biomass (kg ha -1 ) based on % emergent 

wetland (National Wetland Inventory) within a 10 m of 

the waterbody shoreline from Craig(1996): biomasss = 

4.875*(% emergent wetlands) 

< .2 0.2 – 0.6 >0.6 26 Average temperature in July-August to predict juvenile 

survival from Caselman and Lewis 1996): year class 

strength = 1474.81-199.59T +8.97T 2 -0.13T 3 

50 cm 5 Fish growth rate model based on lake morphometric 

measures and water quality from Wagner et al. (2006): 

growth =56.6(TN)-16(Color)+21.1(Mean 

Depth)+1.64(Lake Area)+466.5 

< 6.5m 6.5-13m > 13m 2 39 Fish growth based on water clarity from Casselman and 

Lewis (1996): weight = (Secchi-3)*0.06 

25°C 

19-19°C 

or 21- 

25°C 

19-21°C 2 Average temperature in early summer (Jun e 21 to July 

21) that determines the potential to develop a resident 

> 25% lake 

cover 

1 Parameters not used in the classification because of the lack of water quality data 

population from Casselman and Lewis (1996) 

2 39 Percent macrophyte lake cover through methods 

developed by Hakanson and Boulion (2002): 

%macrophyte cover = (10.49+1.502(Secchi/Mean 

Depth)-1.993(90/90-Latitude)-0.433SQRT(Maximum 

Depth)+0.490(log(Area of lake

Table 5 Northern Pike Waterway Habitat Parameters 

No. Habitat 

Habitat Suitability 

Description 

Parameter 0 0.2 0.4 0.6 0.8 1 

10 Low Flow 16 cm Exclusionary criteria for waterway based on minimum low flow depth 

Minimum Water 

Depth 

using average depth of channel during low flow period. 

11 Maximum >=6.6% = 5 cm/sec < 5 cm/sec Exclusionary criteria from Inskip(1982) based on maximum velocity of 

Velocity 

less than 5 cm/sec for northern pike using average velocity during low 

flow period 

13 Stream Gradient >=0.5% 0.40 0.25 0.20 0.15

(early life stages were weighted more than later life stages) or the reliability of the 

parameter. A weighted rank (weighted sum of each parameter divided by the sum of 

the weights) was developed for each waterbody and classified into low, medium and 

high potential northern pike habitat. 

The waterway model used a variation of that proposed by Inskip (1982) and used only 

stream and river hydraulic characteristics. Hydraulic-geometry relationships (Dudley 

2004 and Wright et al. 2008) were used to approximate waterway channel 

characteristics for the low flow period (average velocity, depth and gradient) for each 

stream or river in the watershed. The classification was completed for stream or river 

segments or reaches to allow for more continuous classification along the length of a 

particular waterway (see Wright et al. 2008). A habitat suitability index was calculated 

from four parameters in Table 5. Three of the parameters (parameters 10-12) were 

exclusionary (either present or absent). Stream gradient (parameter 12) was assigned 

five values ranging from 0 (not suitable) to 1 (most suitable). A habitat suitable index 

(HSI) was developed for each waterway segment by multiplying each of the parameter 

values. The HSI was assigned a value from 0 (not suitable) to 1 (most suitable) for all 

the classified waterway segments. 

Results 

The results for the waterbody and waterway models should be viewed as only indicators 

of the northern pike population-habitat relationships with their primary value being to 

improve decision-making in a structured approach. The models are only one aspect of 

identifying the risk of northern pike introductions and should not be relied upon solely for 

decision making. 

1. Two ponds ranked high (Towne Pond and Oak Knoll Bog) with each pond being 

less than 8 HA in area (20 acres). High ranked waterbodies accounted for about 

1 percent of all the lakes and ponds. 

2. Ninety-four waterbodies ranked as medium potential and ranged from 2 to 582 

HA. About 90 percent were less than 40 HA (about 100 acres). The five largest 

waterbodies ranked as medium potential include: Endless Lake, Ebeemee Lake, 

Burden Pond, Second and Third Branch Ponds, and Shirley Bog. Medium 

ranked waterbodies accounted for 48 percent of all the lakes and ponds. Of 

these, only Ebeemee and Endless will be accessible. All others are above 

Sebec Dams (Burden), waterfalls (second and third WB Ponds) or Dover. 

3. One hundred waterbodies ranked as low potential and ranged from 2 to 2,841 

HA. They accounted for about 51 percent of all the lakes and ponds. About 66 

percent were less than 40 HA (about 100 acres). The five largest waterbodies 

ranked as low potential were: Schoodic Lake, Sebec Lake, Seboeis Lake, Lower 

Wilson Pond and Lake Onawa. 

PRFP Page 238

4. The 40 largest watebodies in the Piscataquis River watershed and their rank are 

listed in Table 6. Figure 9 shows the distribution and location of the ranked 

waterbodies in the watershed. 

Table 6 Piscaquis River Waterbodies Ranked for Northern Pike Habitat Potential 

MIDAS Waterbody Name Area (acre) Area (HA) Rank 

956 Schoodic Lake 7,021 2,841 Low 

848 Sebec Lake 6,362 2,575 Low 

954 Seboeis Lake 4,913 1,988 Low 

942 Endless Lake 1,439 582 Medium 

342 Lower Wilson Pond 1,414 572 Low 

894 Lake Onawa 1,192 482 Low 

314 Bald Mountain Pond 1,146 464 Low 

2130 East Branch Lake 1,122 454 Low 

410 Upper Wilson Pond 987 399 Low 

914 Ebeemee Lake 905 366 Medium 

2004 Cedar Lake 654 265 Low 

916 Big Houston Pond 644 261 Low 

800 Long Pond 644 261 Low 

301 Lake Hebron 638 258 Low 

478 B Pond 610 247 Low 

758 Manhancock Pond 475 192 Low 

262 Kingsbury Pond 432 175 Low 

298 Piper Pond 423 171 Low 

838 First Buttermilk Pond 389 158 Low 

4130 Branns Mill Ponds 352 142 Low 

380 Monson Pond 351 142 Low 

864 Big Benson Pond 332 134 Low 

814 Indian Pond 290 117 Low 

2006 Flatiron Pond 284 115 Low 

922 Silver Lake 279 113 Low 

296 Whetstone Pond 256 104 Low 

780 Rum Pond 232 94 Low 

774 First Davis Pond 216 87 Low 

884 Big Greenwood Pond 210 85 Low 

834 Burden Pond 201 82 Medium 

442 Second and Third Branch Ponds 199 80 Medium 

966 Upper Ebeemee Lake 192 78 Low 

260 Mayfield Pond 188 76 Low 

273 Buttermilk Pond 183 74 Low 

350 Shirley Bog (West) 179 73 Medium 

756 Harlow Pond 179 72 Medium 

368 Spectacle Ponds 178 72 Low 

412 Horseshoe Pond 171 69 Medium 

828 Little Benson Pond 149 60 Medium 

PRFP Page 239

Figure 9 Distribution and location of the ranked northern pike waterbodies in the watershed 

PRFP Page 240

5. About 97 percent of the rivers and streams (2,714 km) in the watershed were 

assigned a HSI value of 0. 

6. Of the 3 percent (97 km) that were assigned a HSI value of 0.2 or higher, most 

were located in the Piscataquis River mainsteam downstream of the Town of 

Guilford and in the lower Sebec and Pleasant Rivers near the confluence of the 

Piscataquis River (Figure 10). 

7. Ninety-four percent of the river segments that were suitable potential habitat for 

northern pike were rated as higher suitability (HSI values of 0.8 or 1). 

Figure 10 Riverine Rank for potential northern pike habitat 

Verification/calibration of the northern pike potential habitat model 

The calibration/verification was completed by: 

1. Normalizing the ratings that Robert VanRiper (MDIFW Biologist, Region B) 

provided for the northern pike lakes in Region B to low, medium and high. 

VanRiper rated the lakes from 0 to 5 according to the following criteria: 

PRFP Page 241

5 - Fishery receives significant angling pressure (25% or more targeting 

fish) with decent catch rate (numbers and size) 

3 - Not principle fishery receiving 10% angling pressure with moderate 

catch rate (numbers and size) 

0 - Present but small fish with potentially large numbers of very small fish 

and few year classes (struggling population) 

2. Comparing the model classification to VanRiper 's ratings and trying to 

improve the classification by changing the parameter weights. 

3. Modifying the lake depth parameter by testing mean lake depth, secchi/mean 

depth, lake area at 1 meter, and proportion of lake area at 1 meter (for littoral 

area). Other parameters, such as slope, water temperature and the use of the 

IFW wading bird and waterfowl habitat instead of NWI were used to try to explain 

or improve the classification. 

No improvements were made over the original model and weightings. The model 

correctly classified 66% percent of the northern pike lakes rated by VanRiper, 

over classified 17% of the lakes (the model predicted a higher potential than the 

rating), and under classified 17% of the lakes (the model predicted a lower 

potential than the rating). Overall, the model conservatively classified 83% of the 

lakes by classifying them correctly or overestimating the lake potential 

(classifying a lake as medium that VanRiper identified as low). 

The five northern pike lakes that were under classified by the model were 

reviewed. Lake areas > 1000 HA, mesotrophic lakes, lakes that stratefy and < 

0.5 meters per year of runoff from watershed are the parameters that most 

predicted the model's under classified lakes in Region B (Ingham, Long, Great, 

Messalonskee and Little North/North Ponds). However, the lake type 

(mesotrophic) may be more indicative of lakes in Region B than Region F. 

Based on this screening criteria, at least three lakes would need to be reviewed 

using best professional judgment: Silver, Upper Ebeemee and Seboeis Lakes. 

They meet some but not all of the screening criteria. 

In July 2009, the regional biologist were asked to review the results of the model 

and assign new ranks where needed and the reason for doing so. Ebeemee 

Lake, Endless Lake, Pond Farm Pond, Seboeis Lake, Silver Lake and Upper 

Ebeemee Lake were all rated as a medium during the professional review rather 

than a low risk based on a healthy pickerel population is established in the lakes, 

and due to the abundance of pike spawning and nursery habitat. 

PRFP Page 242

Human-Caused Introductions 

Background 

There are three primary pathways for northern pike: human-caused introduction; natural 

dispersal through volitional movement; and natural dispersal through non-volitional 

movement. Human-caused introductions are intentional or non-intentional introductions 

of northern pike by people. Natural dispersal through volition movement are 

introductions that occur when northern pike disperse to other locations through 

connected waterways. Natural dispersal through non-volitional movement are 

introductions by other natural means, such as the transport of fish by raptors to water 

bodies that may not have been connected to the waterbody of origin. The record of 

northern pike discovery was analyzed to determine: 1) the pattern of introduction and 

dispersal; 2) the rate for introductions and dispersal through these introductions; and 3) 

the annual probability of an introduction through either pathway. 

The discovery record is a historic account of the year that northern pike were 

discovered in a lake or river. The introduction pathway is most often unobservable so it 

is difficult to be entirely certain of the pathway or the period it took to discovery the 

population (Costello and Solow 2003; Solow and Costello 2004). Nevertheless, 

methods have been developed to model the discovery record to provide insight on the 

process of introduction. This analysis is limited to human-caused and natural dispersal 

through volitional movement and assumes that natural dispersal through non-volitional 

movement (transport by birds) is a minor contribution to northern pike dispersal. 

Method 

The discovery record was developed from the MDIFW database used to track northern 

pike introductions (M. Gallagher, January 2008). The database includes the lake (and 

coordinate location); year of discovery; whether the introduction was confirmed by a 

reliable source; and a MDIFW judgment on whether pike are present in the lake. The 

discovery records were categorized based on the reliability (high, medium and low). 

High reliability means that MDIFW determined that pike presence was likely and 

confirmed; medium reliability was that presence was likely but pike were not confirmed; 

and low reliability was unknown presence and confirmation. Only the records with high 

and medium reliability were used in the analysis (Table 7). 

The pathway for each discovery record was classified as either introduced or dispersal 

by examining the hydrological characteristics of the lake and determining whether it was 

isolated (first recorded occurrence in a watershed, geologically isolated through 

glaciation, or located at a watershed terminus); whether a downstream barrier existed 

that may prevent pike from migrating upstream; and what sources of pike were either 

upstream or downstream of the lake. An assumption was made that the year of 

discovery reflected the actual order of introduction or dispersal so that the discovery 

past discoveries only influence the dispersal pattern. 

All records were classified even if the pathway was unclear. In the Cobbosseecontee 

and Messalonskee Stream watersheds pike were discovered and confirmed in many of 

PRFP Page 243

the lakes during the same year so the pattern of dispersal or introduction could not be 

discerned from either isolation, presence of barriers or sources. In these cases, the 

classification was completed through interviews with the MDIFW regional biologists (J. 

Lucas and S. Davis, Region B). 

The classified discovery record was used to examine the introduction pattern in lakes 

using a qualitative time series approach of mapped discoveries and by developing a 

statistical model of that described the rate of discovery using methods developed by 

Solow and Costello (2004). The model is based on fitting a curve to the cumulative 

number of discoveries over time to produce a discovery curve that follows a Poisson 

distribution. These two approaches were used to describe the pattern of introduction 

and dispersal; the rate for introductions and dispersal through these introductions; and 

the pathway probability. 

The dispersal and establishment in rivers was more difficult to assess using the 

discovery record because it contained few records for the Kennebec and Androscoggin 

Rivers. Instead of using the discovery record to examine the pattern of discovery, the 

comprehensive survey completed by Yoder et al. (2005) from 2002 to 2005 was used to 

understand the dispersal and establishment of northern pike in rivers after having 

become well established in the subwatershed of the Kennebec and Androscoggin 

Rivers. The purpose of these surveys were to develop a fish assemblage assessment 

method for large mainstem rivers and included sampling about 140 miles of the 

Kennebec (2002) and Sebasticook Rivers (2003) between Wyman Lake and 

Merrymeeting Bay and 160 miles of the Androscoggin River (2003) between Lake 

Umbagog and Merrymeeting Bay. The Penobscot River was also extensively sampled 

in 2004 (and more recently in 2008) from the West Branch to Souadabscook Stream 

area. A one kilometer segment of the river was sampled at each site using a 

standardized boat electrofishing sampling methodology. This data was examined for 

the presence or absence of pike. Locations were also identified where multiple age 

classes were found, indicating a resident population as opposed to dispersing fish. 

PRFP Page 244

Table 7 Maine Lake Northern Pike Discovery Record 

MIDAS Lake Town County Confirmed Status Reliability Year Isolated Barrier Source Pathway 

5344 North Pond 1 

Smithfield Kennebec Y Present High 1969 Yes No Introduced 

5274 Great Pond Belgrade Kennebec Y Present High 1980 Dispersal 

5270 Ingham Pond Mount Vernon Kennebec Y Present High 1980 Dispersal 

5272 Long Pond Belgrade Kennebec Y Present High 1980 Dispersal 

5280 Messalonskee Lake Belgrade Kennebec Y Present High 1980 Dispersal 

3102 Umbagog Lake Magalloway Plt Oxford, Coos (NH) Y Present High 1990 Yes Yes No Introduced 

5344 North Pond Rome Kennebec, Somerset Y Present High 1991 No No Yes Dispersal 

3796 Sabattus Pond Greene Androscoggin Y Present High 1994 Yes Yes No Introduced 

3828 Berry Pond Winthrop Kennebec Y Present High 1996 Introduced 

3830 Dexter pond Winthrop Kennebec N Present Medium 1996 Dispersal 

5236 Cobbosseecontee Lake Winthrop Kennebec Y Present High 1996 Dispersal 

9961 Annabessacook Lake Monmouth Kennebec Y Present High 1996 Introduced 

0103 Lower Narrows Pond Winthrop Kennebec Y Present High 1996 Dispersal 

0098 Upper Narrows Pond Winthrop Kennebec N Present Medium 1996 Dispersal 

5252 Horseshoe Pond Litchfield Kennebec N Present Medium 1996 Dispersal 

5254 Pleasant Pond Gardiner Kennebec N Present Medium 1996 Dispersal 

3832 Wilson Pond Wayne Kennebec N Present Medium 1996 Dispersal 

3750 Taylor Pond Auburn Androscoggin Y Present High 1999 Yes Yes No Introduced 

3624 Bear Pond Hartford Androscoggin, Oxford Y Present High 1999 Yes Yes No Introduced 

3624 Little Bear Pond Hartford Oxford Present Medium 1999 Yes Yes No Introduced 

3626 Crystal Pond Turner Androscoggin N Present Medium 2000 No No Yes Dispersal 

3790 Little Sabattus Pond Greene Androscoggin Y Present High 2000 No No Yes Dispersal 

0037 Winnegance Lake Phippsburg Sagadahoc Y Present High 2001 Yes Yes Yes Introduced 

3816 Long Pond Livermore Androscoggin Y Present High 2002 No No Yes Dispersal 

5307 Torsey Pond Mount Vernon Kennebec Y Present High 2002 Yes Yes No Introduced 

5408 Webber Pond Vassalboro Kennebec N Present Medium 2002 Yes Yes No Introduced 

5710 Biscay Pond Damariscotta Lincoln N Present Medium 2002 Yes Yes No Introduced 

3936 Middle Branch Pond Waterboro York Y Present High 2002 Yes Yes No Introduced 

4896 Sheepscot Pond Palermo Waldo N Present Medium 2002 Yes Yes No Introduced 

0007 Estes Lake Sanford York N Present Medium 2002 No Yes Yes Introduced 

4857 Webber Pond Bremen Lincoln Unknown Extirpate High 2003 Yes No No Introduced 

0080 Pushaw Lake Alton Penobscot Y Present High 2003 Yes Yes No Introduced 

5786 Sebago Lake Sebago Cumberland Y Present High 2003 Yes Yes No Introduced 

3836 Androscoggin Lake Wayne Kennebec, Androscoggin N Present Medium 2004 Yes Yes No Introduced 

8065 Little Cobbosseecontee Winthrop Kennebec Y Present High 2004 No No Yes Dispersal 

5176 Lovejoy Pond Albion Kennebec Y Present High 2004 Yes Yes No Introduced 

3818 Round Pond Livermore Androscoggin Y Present High 2005 No No Yes Dispersal 

5222 Nequassett Lake Woolwich Sagadahoc Y Present High 2005 Yes Yes No Introduced 

5650 Mosher Pond Fayette Kennebec Y Present High 2006 Yes Yes No Introduced 

2278 Mud Pond Old Town Penobscot Y Present High 2006 No No Yes Dispersal 

5690 North Pond Warren Knox Y Present High 2007 Yes No No Introduced 

1 Based on a back calculation of when pike were most likely introduced. 

PRFP Page 245

Pattern of Introduction and Dispersal in Lakes 

The pattern of introduction and dispersal in lakes from the discovery record in Table 

6 is graphically illustrated in a map time series in Appendix C. The following results 

were obtained from examining Table 7 and the discovery time series: 

a. The first known occurrence in Maine was documented in North Pond in 

1969 20 . Little North Pond and North Pond are connected and managed as 

the same water. 

b. Forty-one lakes have a medium or high reliability of pike presence. Pike were 

likely introduced in 23 lakes (56%) through human-caused introduction and 

18 lakes (44%) by dispersing from an established source population. 

c. The current pike distribution in Maine has resulted from 23 separate 

unauthorized introductions. 

d. In 10 of the 16 introduced watersheds, pike have not been found to have left 

their original waters or expand their distribution. In four cases, pike moved 

into adjacent waters. In only two watersheds (Cobbosseecontee and 

Messalonskee Stream watersheds) did pike move to any great extent. 

However, both of those watersheds are substantially made up of lakes and 

ponds, and in at least one of these instances, the pike moved downstream 

after being introduced. 

e. The pattern of introductions appears to occur in clusters where several illegal 

introductions will occur in adjacent watersheds within the same time period. 

f. In 15 of 23 introductions, the introductions were the first recorded occurrence 

of pike in the watershed. 

g. There are seven cases where the potential source is identified for which pike 

may have dispersed to another lake. The dispersal period ranged from 1 to 

22 years. The average and medium dispersal period was 7 and 3 years, 

respectively (Table 8). 

Table 8 Northern pike dispersal in Maine lakes 

From Lake Year Discovered To Lake Year Discovered 

Little North Pond 1 

1969 North Pond 1991 

Little Bear and Bear Ponds 1999 Crystal Pond 2000 

Sabattus Pond 1994 Little Sabattus Pond 2000 

Little Bear, Bear and Crystal Ponds 1999/2000 Long Pond 2002 

Cobbosseecontee Lake 1996 Little Cobbosseecontee Lake 2004 

Long Pond 2002 Round Pond 2005 

Pushaw Lake 2003 Mud Pond 2006 

20 Based on a back calculation of when pike were most likely introduced (Little North Pond and North 

Pond are connected and managed as the same water). 

PRFP Page 246

Pattern of Introduction and Dispersal in Rivers 

The pattern of introduction and dispersal in rivers could not be obtained from the 

discovery record because it included few occurrences. The comprehensive surveys 

by Yoder et al. (2005) and any follow-up surveys that were completed as part of this 

work (additional surveys for the Penobscot River in 2008) were used for this 

analysis. The purpose of Yoder’s work was to better understand fish assemblages 

and habitat associations in large rivers (non-wadeable) in Maine and most rivers 

were sampled over much of their entire length. 

1) Yoder et al. (2005) sampled 39 sites on the Kennebec River, 50 sites on the 

Androscoggin River and 31 sites on the Penobscot River (see figures in 

Appendix C). 

2) Northern pike were documented at two sites. One adult pike was captured at 

one site on the Kennebec River and four fish (adult and young-of-year) were 

captured at one site on the Androscoggin River. 

3) One resident population appears to have become established on the 

Androscoggin River near the mouth of the Sabattus River, close to the 

potential source (Sabattus Lake). 

4) No pike were documented in the rivers that were sampled in the Penobscot 

River watershed. Pike were first reported in Pushaw Lake in 2003, confirmed 

in 2005, and confirmed in Mud Pond in 2006. Given the empirical medium 

dispersal period of three years based on the discovery record, the sampling 

may have been early in the pike introduction and failed to detect them and/or 

MDIFW control methods in Pushaw Lake have been successful in limiting 

pike dispersal. 

5) The establishment of pike populations in mainstem rivers appears to occur at 

a much lower rate than in lakes given the limited discoveries of pike in the 

Androscoggin and Kennebec Rivers and the few occurrences found by Yoder. 

Rate and Probability in Lakes 

Methods developed in Solow and Costello (2004) for analyzing the discovery record 

were used to develop a model of the northern pike discoveries in Maine lakes. A 5parameter 

model was fit to the discovery record and then solved using maximumlikelihood 

estimation. This analysis constructed models for two cases. One case 

used only lakes where northern pike were likely introduced through human-caused 

introductions (introduced). The other case used the entire discovery record, 

including lakes where pike were discovered through human-caused introductions or 

from natural dispersal (combined). The probability for introductions through 

dispersal was obtained by the difference of these two models. A model was not able 

to be directly constructed for the dispersal pathway because dispersals were often 

PRFP Page 247

clumped (many documented in one year) and relatively infrequent (occurring over a 

relatively few years for the 30-year record). 

1) The model parameters and maximum-likelihood estimates (MLE) from Solow 

and Costello (2004) for the two cases are: 

Case 

ˆβ 0 

ˆβ 1 

0 ˆ γ 2 ˆ γ 1 ˆ γ 

PRFP Page 248 

MLE 

Introduced -3.3739 0.1208 32.2508 0.0625 0.0467 -21.32 

Combined -2.1520 0.0894 31.9848 0.0436 -0.0032 -22.05 

The data, which are plotted in Figure 11, are for introduced northern pike 

discoveries from 1969 to 2007 and shows the fitted values (smooth line) 

along with the discovery data (dashed line). 

25 

Cu 

20 

mu 

lati 

ve 

Dis 15 

cov 

eri 

es 10 

5 

0 

19 

69 19 

71 19 

73 19 

75 19 

77 19 

79 19 

81 19 

83 19 

85 19 

87 19 

89 19 

91 19 

93 19 

95 19 

97 19 

99 20 

01 20 

03 20 

05 20 

07 

Year 

Figure 11 Northern pike discoveries from human-caused introductions 1969-2007 

2) The estimated mean introduction rate raises from 0.03 introductions per year 

in 1969 to 2.6 introductions per year in 2007. The annual rate of increase is 

about 6.8% per year since 1969. The mean introduction rate in the 1970s, 

1980s, 1990s and 2000s was 0.06, 0.19, and 0.62 and 1.80 introductions per 

year, respectively. 

3) The rate of introduction is not constant nor has it declined over the 30-year 

record. This indicates that programs to decrease human-caused 

introductions may not be effective in controlling this pathway and that these 

introductions may be difficult to control in the future.

4) The model developed by Solow and Costello (2004) has a Poisson 

distribution with an annual introduction rate described by μ t = exp( β 0 + β 1t 

), 

where β 0 and β1 were estimated through a maximum-likelihood method and 

are reported above. The Poisson distribution is useful in describing counts 

from rare events over a continuous timeframe. A Poisson probability density 

function (PDF) can be developed from the annual introduction rate that 

describes the probability of the number of discoveries one could expect for 

that year. The PDF can be used to estimate the probability of the number of 

discoveries occurring in any one year by: 

x 

λ 

P( x) 

= x 

e x! 

where x is the number of discoveries in an interval and λ is the mean rate 

over the interval. For this application, the mean introduction rate in 2007 of 

2.64 introductions was used to determine the current probability for humancaused 

introductions. The probability of northern pike dispersal in any one 

year was constructed by taking the difference (subtracting the two mean rates 

for 2007) of the combined and introduced models. The probability functions 

for human-caused introduction (smooth line) and natural dispersal (dashed 

line) are plotted in Figure 12. 

Annual Probability 

0.4000 

0.3500 

0.3000 

0.2500 

0.2000 

0.1500 

0.1000 

0.0500 

0.0000 

0 1 2 3 4 5 6 7 8 9 10 11 

Number of Introductions 

Human-caused Dispersal 

Figure 12 Probability density functions for human-caused introductions and dispersal of northern pike 

Each curve in Figure 12 represents the probability of an introduction occurring 

in any one year in Maine. Inspection of the PDF for each case provides some 

insights on the risk of each pathway: 

a. The probability of having no introductions (maintaining the current 

condition) is more than four times more likely under natural dispersal ( ρ = 

0.32) than under human-caused introductions ( ρ =0.07). Natural dispersal 

PRFP Page 249

occurs at a lower mean rate (1.15 introductions per year) than humancaused 

introduction (2.63 introductions per year). 

b. There is a high probability that one or more annual introductions will occur 

by either pathway. The annual probability of one or more human-caused 

introductions is very high ( ρ =0.93). The annual probability for one or 

more natural dispersals is also moderately high ( ρ =0.68). When 

comparing the two probabilities, the probability of having one or more 

introductions is 31% higher through human-caused introductions than 

under natural dispersal. 

c. Human-caused introductions are more likely to result in multiple 

introductions in one year than introductions through natural dispersal. The 

probability of three or more introductions in one year is 0.49 for humancaused 

introductions in contrast to a probability of 0.11 for natural 

dispersal. This higher probability may arise from the mechanism of 

dispersal. Human-caused introductions can occur through a watershed in 

watersheds that are disassociated from those that contain northern pike. 

Introductions through natural dispersal occur in watersheds where pike 

are found and more likely to occur in habitat adjacent to or downstream of 

existing populations (J. Casselman, personal communication, March 13, 

2009). 

d. Both pathways pose a risk for introduction of northern pike, however 

human-caused introductions pose a greater risk. They have a very low 

probability of resulting in no introductions in any one year, they have a 

much higher mean rate of introduction, they have a much higher 

probability of multiple introductions in one year, and they can result in 

introductions in watersheds removed from those watersheds with 

populations of northern pike. 

PRFP Page 250

Inventory of Risk Rating for Waterbodies 

In order to determine the extent of resources at risk above Howland, two approaches 

were taken. The first looked at identifying priority resources and associated 

geographic locations areas throughout the drainage, resulting in high, medium and 

low ranks for each HUC 12 watershed. The second looked at barriers to northern 

pike, both natural and anthropogenic. 

Rating for the Resource 

A list of five priority resources was developed (see list below). For each resource, a 

score of 0, 1 or 2 was assigned based on occurrences; the presence of EBTJV high 

quality habitat (0 or 2), cold water management lakes (0,1, or 2), wild salmonids (0,1, 

or 2), species of concern (0 or 2 - American eel data is too spotty to be valuable in 

rating), and the sum of Atlantic salmon habitat normalized for watershed size (0,1, or 

2 - where 0 has the lowest number of habitat units and is not a true zero). These 

scores were summed and rated as Category 1 (high) with four to six occurrences of 

priority resources (30% of the drainage), Category 2 (medium) with one to three 

occurrences of priority resources (65% of the drainage), and Category 3 (low) with 

zero occurrences of priority resources (5% of the drainage), (Figure 13). In addition, 

two connections between the Piscataquis and the West Branch Penobscot were 

identified as concerns: 1) East Branch Lake has a north and south outlet where the 

North flows into the West Branch Penobscot and 2) a large wetland complex 

separates Ebeemee Lake, Sanborn Pond and Upper Jo-Mary Lake. 

High Priority Resource Classes 

• High quality brook trout habitat (see Appendix D): Thorn Brook, Kingsbury 

Stream and Pond, East Branch Pleasant River, Middle Branch Pleasant 

River, West Branch Pleasant River above Silver Lake 

• Wild landlocked salmon, lake trout or brook trout lakes: including Sebec lake 

and Schoodic Lake and Heritage brook trout ponds A (never been stocked) 

and B (not stocked in past 25 years). There are 62 total wild and native brook 

trout ponds in the drainage (Table 9). 

• Species of Concern: Lake whitefish in Hebron Lake, arctic char in Bald 

Mountain Pond as well as American eel throughout the drainage 

• Atlantic salmon: Based on Atlantic salmon habitat model 

• Lake management areas: Cold water management and remote lakes 

Known Barriers to Northern pike 

As identified in the habitat model section of this document, northern pike are not 

adapted to strong currents. Water velocity exceeding 1.5 m/s can block spawning 

migrations (Inskip 1982). Northern pike have little use for riverine habitats where the 

gradient exceeds 5 m/km (0.5 % slope), and have less tolerance for gradient than 

muskellunge (Inskip 1982). However, it was determined that northern pike dispersal 

in Sweden was precluded only when maximum stream slope approached 6.6 % 

(Spens et al. 2007). In addition, renowned fisheries scientist and expert on Northern 

pike, Dr. John Casselman, states that a 30-inch jump is adequate to prevent the 

upstream passage of pike through the fishways (pers. comm.). 

PRFP Page 251

Figure 13 Resource value areas 

Therefore, natural falls and dams where temporary velocity or jump barriers could be 

created were identified (Figure 14 and Table 10). These barriers would be 

considered emergency measures but not permanent solutions, as they would allow 

passage of Atlantic salmon grilse and adults but will severely hinder the passage of 

most native species including anadromous alosids (river herring and American shad) 

and as such should considered a short term solution. The adverse impact on 

anadromous alosids would be minimal in the short term since very few adult alosids 

are currently present below these projects. 

Three main stem dams, Brown's Mill (Dover-Foxcroft Lower), Moosehead 

Manufacturing (Dover-Foxcroft Upper), and Guilford (Interface), exist. All three have 

vertical slot fishways. Only Brown’s Mill has both upstream and downstream 

passage, although all three have upstream passage. The two dams in Dover- 

Foxcroft are hydro-electric facilities. There are also two dams in the Sebec drainage 

(Milo and Sebec) that currently have no provisions for passage. The dam at 

Schoodic Lake has a 6’ dam with three gates – but at high water it may be passable 

and West Seboeis Lake dam is impassible. 

There are also several natural barriers in the drainage. These include a series of 

falls around Gulf Hagas on the West Branch Pleasant, Gauntlet and Mud Gauntlet 

Falls on the East Branch Pleasant, two sets of mapped falls on Ship Pond Stream 

PRFP Page 252

(Buck's Falls and Cowyard Falls), multiple falls on Wilson Stream and its tributaries 

(Early Landing Falls; three unnamed falls just above the confluence with Leeman 

Brook; and Little Wilson Falls) and two falls on the Piscataquis River above Guilford 

(an unnamed set of falls near a picnic area in Blanchard and Hatch Falls on the 

West Branch Piscataquis). 

Figure 14 Natural and human barriers 

PRFP Page 253

Table 9 Wild and Native Brook Trout Ponds 

Lake Watershed Category County 

Baker Pond West Branch Pleasant River (1) at Silver Lake Native: Never been stocked Piscataquis 

Bear Pond Big Wilson Stream (2) Native: Never been stocked Piscataquis 

Bluff Pond West Branch Pleasant River (1) at Silver Lake Native: Never been stocked Piscataquis 

Brown Pond Lake Onawa Native: Never been stocked Piscataquis 

Burden Pond First Buttermilk Pond Native: Never been stocked Piscataquis 

Buttermilk Pond First Buttermilk Pond Native: Never been stocked Piscataquis 

Cedar Pond East Branch Pleasant River (2) Native: Never been stocked Piscataquis 

Crockett Pond Thorn Brook Native: Never been stocked Piscataquis 

Duck Pond First Buttermilk Pond Native: Never been stocked Piscataquis 

East Chairback Pond Long Pond Native: Never been stocked Piscataquis 

Gauntlet Pond East Branch Pleasant River (2) Native: Never been stocked Piscataquis 

Greenwood Pond White Brook Native: Never been stocked Piscataquis 

Grenell Pond Lower Wilson Pond Native: Never been stocked Piscataquis 

Hedgehog Pond Long Pond Native: Never been stocked Piscataquis 

Hutchinson Pond East Branch Pleasant River (1) Native: Never been stocked Piscataquis 

Indian Pond Big Wilson Stream (1) at Bodfish Native: Never been stocked Piscataquis 

Ira Bog Shirley Pond Native: Never been stocked Piscataquis 

Juniper Knee Pond Little Wilson Stream Native: Never been stocked Piscataquis 

Little Benson Pond Ship Pond Stream Native: Never been stocked Piscataquis 

Little Grapevine Pond Sebec Lake (1) at Narrows Native: Never been stocked Piscataquis 

Little Moxie Pond West Branch Piscataquis River Native: Never been stocked Somerset 

Little Wilson Pond Little Wilson Stream Native: Never been stocked Piscataquis 

Lower Doughty Pond East Branch Piscataquis River Native: Never been stocked Piscataquis 

Marble Pond West Branch Piscataquis River Native: Never been stocked Piscataquis 

Middle Branch Pond Middle Branch Pleasant River Native: Never been stocked Piscataquis 

Mill Brook Pond Sebec Lake (2) at Sebec Native: Never been stocked Piscataquis 

Moose Pond Little Wilson Stream Native: Never been stocked Piscataquis 

Mountain Brook Pond West Branch Pleasant River (1) at Silver Lake Native: Never been stocked Piscataquis 

Mountain View Pond East Branch Pleasant River (1) Native: Never been stocked Piscataquis 

Notch Pond Lower Wilson Pond Native: Never been stocked Piscataquis 

Ordway Pond West Branch Piscataquis River Native: Never been stocked Piscataquis 

PRFP Page 254

Prescott Pond Little Wilson Stream Native: Never been stocked Piscataquis 

Punchbowl Pond Thorn Brook Native: Never been stocked Piscataquis 

Round Pond East Branch Pleasant River (1) Native: Never been stocked Piscataquis 

Rum Pond Lower Wilson Pond Native: Never been stocked Piscataquis 

Secret Pond Lake Onawa Native: Never been stocked Piscataquis 

Spruce Mtn Ponds-West Silver Lake Native: Never been stocked Piscataquis 

Trout Pond Long Pond Native: Never been stocked Piscataquis 

unnamed pond Bald Mountain Pond Native: Never been stocked Somerset 

Upper Doughty Pond East Branch Piscataquis River Native: Never been stocked Piscataquis 

West Chairback Pond Big Houston Pond Native: Never been stocked Piscataquis 

1st Little Lyford Pond West Branch Pleasant River (1) at Silver Lake Wild: No direct stocking since 1983 Piscataquis 

2nd Little Lyford Pond West Branch Pleasant River (1) at Silver Lake Wild: No direct stocking since 1983 Piscataquis 

B Pond B Pond Wild: No direct stocking since 1983 Piscataquis 

Big Benson Pond Ship Pond Stream Wild: No direct stocking since 1983 Piscataquis 

Big Lyford Pond West Branch Pleasant River (1) at Silver Lake Wild: No direct stocking since 1983 Piscataquis 

Dow Pond Piscataquis River (3) above Sebec River Wild: No direct stocking since 1983 Piscataquis 

First West Branch Pond West Branch Pleasant River (1) at Silver Lake Wild: No direct stocking since 1983 Piscataquis 

Fogg Pond Lower Wilson Pond Wild: No direct stocking since 1983 Piscataquis 

Foss Pond Thorn Brook Wild: No direct stocking since 1983 Piscataquis 

Horseshoe Pond Lower Wilson Pond Wild: No direct stocking since 1983 Piscataquis 

Little Houston Pond Houston Brook Wild: No direct stocking since 1983 Piscataquis 

Long Pond Wild: No direct stocking since 1983 Piscataquis 

Mountain Pond Lower Wilson Pond Wild: No direct stocking since 1983 Piscataquis 

Mud Greenwood Pond Wild: No direct stocking since 1983 Piscataquis 

North Pond Big Wilson Stream (2) Wild: No direct stocking since 1983 Piscataquis 

Second Buttermilk Pond First Buttermilk Pond Wild: No direct stocking since 1983 Piscataquis 

Second West Branch Pd West Branch Pleasant River (1) at Silver Lake Wild: No direct stocking since 1983 Piscataquis 

Spectacle Pond Thorn Brook Wild: No direct stocking since 1983 Piscataquis 

Third West Branch Pond West Branch Pleasant River (1) at Silver Lake Wild: No direct stocking since 1983 Piscataquis 

Upper Wilson Pond Lower Wilson Pond Wild: No direct stocking since 1983 Piscataquis 

PRFP Page 255

Table 10 Piscataquis River Watershed Ponds With Outlet Barriers 

Name Type River Owner 

East Davee Brook Site #3 Dam Snows Pond 

Kingsbury Dam Dam KINGSBURY STREAM TOWN OF KINGSBURY 

Pingree Dam Dam PINGREE STREAM ROBERT TIPTON 

Branns Pond Dam Dam BLACK STREAM TOWN OF DOVER FOXCROFT 

Shirley Pond Dam Dam EAST BRANCH PISCATAQUIS RIVER TOWN OF SHIRLEY 

Phillips Brooks Dam Dam TR MONSON STREAM TOWN OF MONSON 

Big Bennett Pond Outlet Dam BENNETT BROOK SEBEC LAKE FISH+GAME ASS 

Sebec Dam Dam SEBEC RIVER BANGOR HYDRO ELECTRIC CO 

Schoodic Lake Dam Dam SCHOODIC STREAM BANGOR HYDRO ELECTRIC CO 

Milo Dam Dam SEBEC RIVER TOWN OF MILO 

Pond Farm Pond Dam Dam TR-SEBOEIS STREAM STATE OF ME DIFG 

Lower Wilson Pond Dam Dam BIG WILSON STREAM GREENVILLE MFG CO 

Pestock Dam Dam BIG WILSON STREAM GREENVILLE MFG CO 

Seboeis Dam Dam WEST BRANCH SEBOEIS STREAM BANGOR HYDRO ELECTRIC CO 

Lower Dam Dam PISCATAQUIS RIVER TOWN OF DOVER FOXCROFT 

Dunham Brook Site 2 Dam Dunham Brook 

Davee Brook #1 Dam Davee Brook 

Upper Dam Dam PISCATQUIS RIVER TOWN OF DOVER-FOXCROFT 

Carlton Stream Dam Dam CARLTON STREAM NUMBER ALL INC 

Manhanock Pond Dam Dam CARLTON STREAM HALEY CONSTRUCTION CO 

Manhanock Pond Dam Dam CARLTON STREAM TOWN OF SANGERVILLE 

First Davis Pond Dam Dam DAVIS BROOK DIAMOND INTERNATIONAL CO 

Guilford Industries Dam Dam PISCATAQUIS RIVER GUILFORD INDUSTRIES INC 

Bennett Pond Dam Dam Gales Brook 

Piper Pond Dam Dam Kingsbury Stream 

Buttermilk Falls Falls 

Gauntlet Falls Falls 

Cowyard Falls Falls 

Toby Falls Falls 

Monson Stream Falls Falls 

Garland Pond Outlet Dam Dam 

Little Houston Pond Impass block 

Mountain Brook Pond Falls Falls 

Cedar Pond Barrier block 

Gauntlet Pond Barrier block 

Mill Brook Pond Impass block 

West Chairback Pond Ledges block 

Eighteen Pond Falls Falls 

Cranberry Pond Impass block 

Notch Pond Impass block 

Little Wilson Falls Falls 

Earley Landing Falls Falls 

Bucks Falls Falls 

Hatch Falls Falls 

Key Conclusions 

PRFP Page 256

Summary of Ecological Risk 

Introductions of large, top-predators such as northern pike (Esox lucius) negatively 

affect resident fish communities by disrupting normal feeding behavior (Bystrom et 

al. 2007), decreasing prey biomass and abundance (He and Kitchell 1990; Findlay et 

al. 2005) and through extirpation of native species (Findlay et al. 2005; Bystrom et 

al. 2007). Since 1985, the number of northern pike waters has increased from six to 

49 (with 17 expected and one extirpated) statewide (Lucas 2008), representing 

72,789 acres in lake surface area. Invasions or introductions of top predators into 

new ecosystems have been shown to have negative effects on native top predators 

and dramatic cascading effects on lower trophic levels (Vander Zanden et al. 2004). 

Several studies have attributed large losses of stocked and migrating salmonids to 

pike predation in riverine ecosystems. 

A barrier to pike in the existing fishway at the Browns Mill Project in South Dover 

would protect approximately 80% of the stocked salmonid area from the 

establishment of pike through natural dispersal. 

Pike are known to prefer soft-rayed fish as forage (Petrvozvanskiy 1988; Hakanson 

2002), including stocked salmonids, and therefore, it is likely that there will be 

impacts on the stocked brook trout fisheries in these river systems. Since young 

pike do occasionally occur in small streams that have a source of coldwater and they 

prefer soft-rayed fish there could be impacts at the local level for wild trout 

populations, through direct predation or competition for thermal refuge. 

There is considerable niche overlap between northern pike and brook trout in 

lacustrine habitat. Both prefer the littoral zone and both may seek cool water during 

the warmest periods of the summer. Direct predation is possible in situations where 

pike and brook trout occupy the same areas, as well as competition for forage, such 

as minnow species and rainbow smelts. 

The potential for northern pike to adversely impact landlocked salmon populations is 

higher in lakes than in rivers and streams primarily because of the differing habitat 

requirements between the two species. Predation of salmon by pike could be a 

factor at habitat edges. In addition, juvenile salmon may be vulnerable to predation 

by adult pike if the migration route involves long stretches of dead water suitable for 

adult pike or in the lake until they reach an adequate size to escape being eaten. 

Competition for forage may exist between salmon and pike in lakes, particularly if 

forage is limited resulting in a situation where both species are relying heavily upon 

rainbow smelt. 

The impact of Northern pike on populations of lake trout (togue) will likely be low, as 

togue thrive in oligotrophic lakes and Northern pike tend to do better in mesotrophic 

lakes. 

At the youngest juvenile life stages of Atlantic salmon and northern pike, there is no 

evidence for potential habitat overlap. With the onset of spring, longer days and 

PRFP Page 257

warmer waters stimulate mature pike to congregate near river and stream inlets in 

preparation for spawning. At this time, salmon smolts may be at the greatest risk, 

since they are going through physiological changes preparing them for a down river 

migration through many varying habitats. 

There are two connections between the Piscataquis and the West Branch 

Penobscot were identified as concerns: 1) East Branch Lake has a north and south 

outlet where the North flows into the West Branch Penobscot and 2) a large wetland 

complex separates Ebeemee Lake, Sanborn Pond and Upper Jo-Mary Lake. 

Model Limits and Summary 

Measures were developed as critical habitat parameters based on: 1) the literature 

on the habitat requirements of northern pike and 2) the availability of data in Maine 

available for the watershed. The habitat parameters were developed first and then 

applied without prior knowledge or through the direct use of the waterbody/waterway 

characteristics. 

The results for the waterbody and waterway models should be viewed as only 

indicators of the northern pike population-habitat relationships with their primary 

value being to improve decision-making in a structured approach. The models are 

only one aspect of identifying the risk of northern pike introductions and should not 

be relied upon solely for decision making. 

1. Two ponds ranked high (Towne Pond and Oak Knoll Bog) with each pond 

being less than 8 HA in area (20 acres 

2. 94 waterbodies ranked as medium potential and ranged from 2 to 582 HA. 

About 90 percent were less than 40 HA (about 100 acres). The five largest 

waterbodies ranked as medium potential include: Endless Lake, Ebeemee 

Lake, Burden Pond, Second and Third Branch Ponds, and Shirley Bog. 

3. 100 waterbodies ranked as low potential and ranged from 2 to 2,841 HA. The 

five largest waterbodies ranked as low potential were: Schoodic Lake, Sebec 

Lake, Seboeis Lake, Lower Wilson Pond and Lake Onawa. 

4. About 97 percent of the rivers and streams (2,714 km) in the watershed were 

assigned a HSI value of 0. 

5. Of the 3 percent (97 km) that were assigned a HSI value of 0.2 or higher, 

most were located in the Piscataquis River mainsteam downstream of the 

Town of Guilford and in the lower Sebec and Pleasant Rivers near the 

confluence of the Piscataquis River. 

6. Ninety-four percent of the river segments that were suitable potential habitat 

for northern pike were rated as higher suitability (HSI values of 0.8 or 1). 

The calibration/verification was completed by normalizing the ratings that Robert 

VanRiper (MDIFW Biologist, Region B) provided for the northern pike lakes in 

Region B. The model classification was compared to to VanRiper 's ratings and 

trying to improve the classification by changing the parameter weights. 

PRFP Page 258

No improvements were made over the original model and weightings. The model 

correctly classified 66% percent of the northern pike lakes rated by VanRiper, over 

classified 17% of the lakes (the model predicted a higher potential than the rating), 

and under classified 17% of the lakes (the model predicted a lower potential than the 

rating). Overall, the model conservatively classified 83% of the lakes by classifying 

them correctly or overestimating the lake potential (classifying a lake as medium that 

VanRiper identified as low). 

The five northern pike lakes that were under classified by the model were reviewed. 

Lake areas > 1000 HA, mesotrophic lakes, lakes that stratefy and < 0.5 meters per 

year of runoff from watershed are the parameters that most predicted the model's 

under classified lakes in Region B (Ingham, Long, Great, Messalonskee and Little 

North/North Ponds). However, the lake type (mesotrophic) may be more indicative of 

lakes in Region B than Region F. Based on this screening criteria, at least three 

lakes would need to be reviewed using best professional judgment: Silver, Upper 

Ebeemee and Seboeis Lakes. They meet some but not all of the screening criteria. 

Human Dispersal 

Natural dispersal occurs at a lower mean rate (1.15 introductions per year) than 

human-caused introduction (2.63 introductions per year). Human-caused 

introductions are more likely to result in multiple introductions in one year than 

introductions through natural dispersal. The probability of three or more 

introductions in one year is 0.49 for human-caused introductions in contrast to a 

probability of 0.11 for natural dispersal. This higher probability may arise from the 

mechanism of dispersal. Human-caused introductions can occur through a 

watershed in watersheds that are disassociated from those that contain northern 

pike. Introductions through natural dispersal occur in watersheds where pike are 

found and more likely to occur in habitat adjacent to or downstream of existing 

populations (J. Casselman, personal communication, March 13, 2009). 

Both pathways pose a risk for introduction of northern pike, however human-caused 

introductions pose a greater risk. They have a very low probability of resulting in no 

introductions in any one year, they have a much higher mean rate of introduction, 

they have a much higher probability of multiple introductions in one year, and they 

can result in introductions in watersheds removed from those watersheds with 

populations of northern pike. 

Summary of Resources at Risk 

In order to determine the extent of resources at risk above Howland, two approaches 

were taken: identifying priority resources and associated geographic locations areas 

throughout the drainage, and barriers to northern pike, both natural and 

anthropogenic. 

A list of five priority resources was developed. High priority resource classes 

include: high quality brook trout habitat, wild landlocked salmon, lake trout or brook 

trout lakes, species of Concern (Lake whitefish in Hebron Lake, arctic char in Bald 

PRFP Page 259

Mountain Pond as well as American eel throughout the drainage), Atlantic salmon, 

and Cold water management and remote lakes. Occurrences of priority resources 

were summed and rated as Category 1 (high) with four to six occurrences of priority 

resources (30% of the drainage), Category 2 (medium) with one to three 

occurrences of priority resources (65% of the drainage), and Category 3 (low) with 

zero occurrences of priority resources (5% of the drainage). 

Northern pike are not adapted to strong currents. Water velocity exceeding 1.5 m/s 

can block spawning migrations (Inskip 1982). Northern pike have little use for 

riverine habitats where the gradient exceeds 5 m/km (0.5 % slope), and have less 

tolerance for gradient than muskellunge (Inskip 1982). Therefore, natural falls and 

dams where temporary velocity or jump barriers could be created were identified. 

These barriers would be considered emergency measures but not permanent 

solutions. 

Tiered Risk Approach 

In order to articulate the risk, the drainage was divided into three areas; 1) areas 

where barriers exist and some action is possible, 2) areas without barriers that have 

Category 1 resources and 3) areas without barriers that are category 2 or 3. 

Level 1 Management actions 

Locations where potential action can be taken are areas that are either above 

natural barriers or above a human barrier that can be modified where Category 1 

resources are at risk. The risk of natural northern pike dispersal in these areas is 

low. 

• The Sebec drainage has two FERC regulated dams (Milo and Sebec) below 

the outlet that currently have no provisions for passage. 

• The upper Piscataquis River has three dams where temporary velocity or 

jump barriers can be installed; Lower Dover-Foxcroft, Upper Dover-Foxcroft 

and Guilford, which all currently have passage. 

• The dam at Schoodic Lake has a 6’ dam with three gates – but at high water 

it may be passable and West Seboeis Lake dam is impassible. 


Vulnerable areas with Category 1 resources are the highest concern. This category 

comprises 41% of accessible river habitat and 18% of accessible lake habitat 

drainage below natural falls or dams. 

• East Branch Pleasant and East Branch of the Seboeis are the two 

tributaries of the Piscataquis River that have the potential connections to 

the West Branch. 

• Dow Pond is the only native/wild brook trout pond below an existing 

barrier. 

• Some restrictions on passage where possible that are compatible with 

phased alewife and shad restoration goals. 

PRFP Page 260


These areas are the lowest concern in the drainage. This category comprises 59% 

of accessible river habitat and 82% of accessible lake habitat drainage below natural 

falls or dams. 

• Suggest monitoring in these areas 

• Public education 

• No restrictions on passage 

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Management Actions 

2009: 

a. Maintain current blockages for pike in Sebec upper and lower until phase 1 of 

alewife restoration is complete and group 1 American shad restoration is 

complete. 

a. Develop an MOU to re-visit in 2014 

b. Investigate and maintain current blockages for pike in Schoodic and Seboeis 

Lakes until phase 1 of alewife restoration is complete and group 1 American 

shad restoration is complete. 

a. Investigate current structures 

b. Develop plan of action for modification if necessary 

c. Develop an evaluation plan 

d. Develop a maintenance plan 

e. Develop an MOU to revisit in 2014 

c. Create velocity or jump barriers for pike while allowing Atlantic salmon to pass 

in D-F upper and lower and Guilford lower until phase 1 of alewife restoration 

is complete and group 1 American shad restoration is complete 

a. Investigate current structures 

b. Develop plan of action for modification if necessary 

c. Develop an evaluation plan 

d. Develop a maintenance plan 

e. Develop an MOU to revisit in 2014 

d. Third party survey of potential connections and a development of solutions 

between the West Branch Penobscot River and the Pleasant River 

(Immediate need) - $15,000 

a. Upper Ebeemee and Upper Jo-Mary Lake (the West Branch 

Penobscot) 

b. East Branch Pond, which flows north and south to Nollesemic to Shad 

to the West Branch Penobscot below two impassable dams. 

e. Continue removal efforts at Pushaw - IFW cost one time $30,000 plus annual 

salary. 

a. Conduct a study of Pushaw Stream to look for juvenile pike 

f. Conduct a study of Mud Pond 

g. E-fish around the known spawning areas to look for nursery areas. 

h. Review current fishing regulations and develop recommendations for 

changes. 

i. Review current education efforts and develop recommendations for changes. 

j. Maintain public education efforts highlighting the permanent repercussions 

and costs associated with illegal fish stocking events. 

2010: 

b. Continue removal efforts at Pushaw - annual IFW cost 

c. If feasible, install barriers between the Pleasant River and the West Branch 

Penobscot River – Cost TBD 

PRFP Page 262

d. Conduct habitat surveys of the Penobscot mainstem from Milford to Howland 

to determine the spatial distribution, quantity and quality of habitat patches 

necessary for upstream pike dispersal. 

e. LIDAR survey for gradient to get better data on potential movement of pike 

and location of additional natural barriers. 

f. Implement changes to the fishing regulations 

g. Enhance educational efforts to reduce human introductions 

2011: 

a. Continue removal efforts at Pushaw - annual IFW cost 

b. Design a stratified random survey for non-natives in the drainage 

2012: 

a. Continue removal efforts at Pushaw - annual IFW cost 

b. Implement the non-native survey 

PRFP Page 263

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adult pik (Esox lucius L.) in a lowland river. Ecology of Freshwater Fish 15: 

191-199. 

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Lucas, J. 2008. Revised: Northern Pike Management Plan. Maine Department of 

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Wildlife Management. Interaction Book Company, Minnesota. 253 pp. 

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Appendices 

Appendix A: Trapping/Sorting/Counting Facility Proposed Bypass Channel Howland 

Dam, Howland, Maine. May 20, 2008 

Appendix B: A handout summarizing Stantec’s evaluation was distributed at the 

meeting and is included as 

Appendix C: The pattern of introduction and dispersal in lakes from the discovery 

record graphically illustrated in a map time series 

Appendix D: Invasive species response and the Eastern Brook Trout joint Venture 

(EBTJV) 

PRFP Page 268

Appendix A: Trapping/Sorting/Counting Facility Proposed Bypass Channel 

Howland Dam, Howland, Maine. May 20, 2008 

PRFP Page 269

1 INTRODUCTION 

This report presents preliminary information and comments regarding the feasibility of a 

facility for trapping, sorting, and counting of fish passing upstream in the proposed bypass 

channel (Proposed Bypass) at Howland Dam on the Piscataquis River adjacent to its 

confluence with the Penobscot River in Howland, Maine. The Proposed Bypass channel is 

identified in the Lower Penobscot River Basin Comprehensive Settlement Accord as a 

PRFP Page 270

means to “provide safe, timely and effective fish passage sufficient to allow the fisheries 

management goals and objective of the Resource Agencies and PIN to be met.” 

During the spring and summer of 2007, representatives of the Penobscot River Restoration 

Trust (Trust) met with state and federal fisheries agency staff to develop an Outline for 

Preliminary Design of Proposed Howland Fish Bypass (Outline). The Outline included a 

provision that: 

“The preliminary design will also evaluate the feasibility and costs (including operating costs) 

of incorporating provisions for trapping/sorting/counting of fish using the bypass. This 

includes measures to exclude upstream migration of northern pike and black crappie, both 

of which do not now exist above the Howland Dam, and are considered by Maine 

Department of Inland Fisheries and Wildlife to be undesirable, non-native invasive species. 

Under the terms of the Settlement Agreement, the resource agencies are responsible for 

management activities such as trapping/sorting/trucking.” 

This letter is intended to address those concerns. The original intent of the Proposed 

Bypass was to provide simple, safe, low maintenance upstream and downstream fish 

passage for all species, all of the time. This report was prepared using conceptual design 

information prepared by Milone & MacBroom, Inc. (MMI) and presents information relevant 

to the general feasibility of a trapping/sorting/counting facility (TSCF). The intent of the 

conceptual TSCF design discussed herein is to present general components of a TSCF 

relevant to the determination of the feasibility of a TSCF. 

A TSCF within the Proposed Bypass was identified by the Trust, in consultation with state 

and federal regulatory authorities, as a means to (1) trap and survey upstream-migrating 

fish; and (2) exclude non-native fishes. As presented here, a TSCF system is an integrated 

system for trapping, sorting, and counting fish passing upstream and providing downstream 

conveyance for flow in the Proposed Bypass. The conceptual TSCF presented here 

therefore consists of appurtenances intended to provide means to trap fish passing 

upstream and to provide for conveyance of water into the Proposed Bypass. 

This study was being performed as part of the ongoing work by MMI on the dam removal 

design for Veazie Dam and Great Works Dam on the Penobscot River and the design of a 

bypass channel at Howland Dam. Information presented in this report was developed from 

information obtained as part of the ongoing project work, collaboration with Dr. Alex Haro of 

the U.S Geological Survey, and comments and suggestions by participants during the 

March 11, 2008, project teleconference. 

2 OBJECTIVES 

The primary objective of the Proposed Bypass is to provide safe, timely, and effective 

upstream and downstream passage for target diadromous fishes, including anadromous 

Atlantic salmon (Salmo salar), American shad (Alosa sapidissima), alewife (Alosa 

pseudoharengus), blueback herring (Alosa aestivalis), and sea lamprey (Petromyzon 

marinus), and catadromous American eel (Anguilla rostrata). Adult fish represent the target 

life-stage for upstream passage of the anadromous species. Target life stages for upstream 

passage of American eel include both the “elver” and “yellow” phases. These fish are herein 

collectively referred to as the target passage species. Multiple life stages of the target 

diadromous fishes may also use the Proposed Bypass for downstream passage. 

PRFP Page 271

A TSCF is considered here as an appurtenance to the Proposed Bypass to provide a means 

for exclusion of non-indigenous fishes, including northern pike (Esox lucius) and black 

crappie (Pomoxis nigromaculatus). These two species are herein collectively referred to as 

target exclusion species. Relevant information documenting the presence of northern pike in 

the Penobscot River watershed is presented in the Pushaw Lake Fisheries Management 

Plan. This report documents the presence of illegally-introduced northern pike in Pushaw 

Lake, which is a tributary to the Penobscot River, along with anecdotal reporting of northern 

pike in the Penobscot River adjacent to Howland Dam. 

Overlapping swimming abilities of the target passage species and the target exclusion 

species preclude achieving the project objectives of upstream fish passage and exclusion 

solely through the design of a bypass channel. Exclusion of non-native fishes is therefore 

the objective of the TSCF facility. 

The TSCF performance criterion is total (100 percent) exclusion of the target exclusion 

species. The need for total exclusion is based on the assumption that introduction of even 

small numbers of target exclusion species may result in reproduction in the Piscataquis 

River watershed upstream from Howland Dam. 

3 CONCEPTUAL DESIGN 

A conceptual design of a TSCF was developed for the Proposed Bypass, including general 

features and operational methods. The basis for this design is that total exclusion of the 

target exclusion species cannot be achieved through the design of the Proposed Bypass 

and therefore manual sorting of upstream passing fishes is required. As previously noted, 

overlapping swimming abilities of the target passage and exclusion species preclude 

exclusion based on hydraulic conditions in the Proposed Bypass. 

A general requirement of the system would be that all or most of the flow be routed through 

the TSCF trapping component during periods of low flow to maintain upstream fish passage 

during these periods. 

Alternative means for excluding the target exclusion species, such as electrical barriers, 

were briefly considered as part of this analysis but were determined to be incapable of 

achieving total exclusion. 

3.1 Overview 

This section presents a general overview of the conceptual TSCF. The conceptual TSCF 

includes a trapping system with an adjacent sorting area located on the right (northwest) 

side of the upstream limit of the Proposed Bypass. 

Based on a review of information presented in the Conceptual Design Plans by MMI dated 

March 2008 and other relevant materials, routing the entire flow of the Proposed Bypass 

through a TSCF does not appear to be practical. The proposed design therefore provides for 

routing of limited attraction flow through the trap system and the balance of the flow entering 

the Proposed Bypass over an adjacent weir. The weir would be designed to preclude 

upstream passage by some or all of the target passage species and all of the target 

exclusion species. The balance of the flow would be routed around the trapping facility 

through the TSCF conveyance channel with means to preclude upstream passage of all 

target species or allow upstream passage for a subset of target passage species. The only 

target passage species capable of upstream passage over a weir designed to exclude 

northern pike would be Atlantic salmon. Alewife and American shad are expected to 

PRFP Page 272

comprise the majority of fish passing upstream through the Proposed Bypass following 

implementation of restoration projects in the Penobscot River watershed, and operation of 

the TSCF would therefore require handling of these fish. 

Fish entering the trap system would be manually sorted with dip nets or similar equipment. 

Manual operations would require skilled staff on a daily basis while target restoration 

species are active. As presented herein, the TSCF can be used for both single and twostage 

manual sorting of trapped fish. It is envisioned that two-stage sorting would be used 

initially to provide for the evaluation of sorting efficacy at excluding target exclusion species. 

Configuration of the sorting area for single or two-stage sorting would be accomplished 

through opening and closing gates between the sorting area immediately adjacent to the 

trap and the hydraulic inlet to the TSCF in the Howland Dam impoundment on the 

Piscataquis River. Trash racks or other means of excluding debris from the TSCF and/or 

Proposed Bypass may be necessary. 

3.2 Facility Details 

This section presents more-detailed information on the TSCF, including design alternatives 

and facility operations. 

3.2.1 Location 

Site-specific factors and functional considerations suggest that a facility located towards the 

upstream end of the Proposed Bypass would be most appropriate. This determination is 

based on biological factors, the generally steep banks downstream from Howland Dam, 

potential flooding of a facility situated adjacent to the confluence of the Piscataquis and 

Penobscot Rivers, and constructability. 

Location of a TSCF along the upper reach of the Proposed Bypass has a number of 

apparent practical advantages over a system located along the downstream reach of the 

bypass channel. 

Installation of a TSCF on the upper reach of the Proposed Bypass would likely result in 

fewer fish dropping back through the Proposed Bypass, particularly if flow speeds are lower 

in the Proposed Bypass upstream from the TSCF. Locating the TSCF at the upstream end 

of the Proposed Bypass along the Howland Dam impoundment would apparently minimize 

the potential for fish dropping-back through the TSCF. Appropriate conditions for upstream 

fish passage upstream from the TSCF are also necessary to reduce impingement of fish on 

the TSCF appurtenances (e.g., bar racks). Locating the TSCF along the upper reach of the 

Proposed Bypass may also limit the number of fish entering the system, as weak and/or 

injured fish and fish that lack a strong urge to move upstream through the system may not 

move far enough up the bypass channel to reach the TSCF. 

The high steep banks downstream from the Howland Dam pose a number of practical 

issues relevant to the TSCF, including potential flooding, constructability, access, and 

operations and maintenance. Potential flooding constraints can be determined using typical 

engineering methods, and would need to consider maximum water surface elevations in the 

Penobscot River and potential overwashing of the adjacent land during flood events in the 

Piscataquis River. Permanent access for heavy equipment to the TSCF would likely be 

required, including tank trucks for “trap and truck” stocking. A TSCF located on the upper 

reach of the Proposed Bypass would likely have easier access for such equipment. 

PRFP Page 273

Because a TSCF would likely result in high concentrations of fish immediately downstream 

of the facility during periods of peak migration, the possibility of poaching should also be 

considered. In addition to providing conditions (e.g., deep water, limited access) that are not 

favorable to poaching, a location in a more visible area would also likely limit poaching. 

3.2.2 Trapping Facility Size 

A primary factor for determining the size of the TSCF is the number of fish requiring sorting 

at the facility during the peak migration periods of diadromous and resident fish. Peak daily 

numbers of fish will likely occur during the upstream migrations of adult alewife, blueback 

herring, and shad in May and June following implementation of restoration projects (e.g., 

removal of Veazie Dam and Great Works Dam) in the Penobscot River. 

Large numbers of seasonally-migrating resident fish, such as white sucker (Catostomus 

commersoni), may also use the Proposed Bypass, and may represent the largest number of 

fish passing through the Proposed Bypass prior to the implementation of the full suite of 

restoration projects in the Penobscot River watershed. 

Estimates have been developed by others 21 of potential numbers of alewife and American 

shad for the Piscataquis River. This information indicates that up to 245,000 adult shad may 

pass upstream at Howland Dam. Estimated adult alewife production for waterbodies in the 

Piscataquis, Pleasant, Schoodic, Sebec, and Seboeis subwatersheds is in excess of 

5,500,000. The upstream migration period for shad and alewife in the Penobscot River 

watershed is from May through June, or approximately 60 days, and it is therefore assumed 

that in excess of 100,000 fish may attempt to move upstream at Howland Dam in a given 

day (4,200 per hour). 

Based on a minimum volume of 0.25 cubic-feet (CF) per pound of fish, an average alewife 

weight of 0.5 pounds, and a maximum passage rate of two-times the hourly passage 

number given above (8,400 fish), the TSCF trap would need to have a volume of 

approximately 1,000 CF. A “holding area” would likely be necessary in the adjacent reach of 

the Proposed Bypass to provide a buffer for potential numbers of fish exceeding the 

handling capacity of the TSCF. 

A proposed guideline for the holding area is that it accommodate two-times the daily 

passage rate of 100,000 fish (200,000 fish) in a given 24-hour period. A volume of 

approximately 25,000 CF would therefore be required, which could be accomplished with a 

holding area of approximately 0.25 acres with an average depth of 2 feet. Provisions for this 

holding area obligate substantial additional areas of land for construction, and behavioral 

response may delay upstream fish migration. 

3.2.3 Weir 

The TSCF weir would need to be sized to preclude upstream passage by the target 

exclusion species for all hydrologic scenarios. Little information is available regarding the 

leaping ability of northern pike, which is the largest of the target exclusion species and 

therefore used here as the basis for exclusion at leaping barriers. The relatively large body 

size of northern pike and associated potential for relatively high burst swimming speeds was 

used here to set a hydraulic barrier height of approximately 10 feet to achieve total 

21 Strategic Plan for the Restoration of Diadromous Fishes to the Penobscot River (Draft 2-26-08), 

prepared by Gail Wippelhauser and Melissa Laser, Maine Department of Marine Resources, and MikeSmith and Richard Dill, 

Maine Department of Inland Fisheries and Wildlife 

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exclusion. Information from published literature was not located to document this 

assumption. 

Based on the approximately 14-foot difference in elevation between the Penobscot River 

and the Howland Dam impoundment at normal flow conditions, a 10-foot high hydraulic 

barrier integrated into the TSCF would reduce rise of the Proposed Bypass from 14 to 4 feet 

at normal flows. Changes to this head differential during periods of high flow would need to 

be evaluated to determine whether increased backwater effects would adversely affect the 

efficacy of the hydraulic barrier at the weir. 

The use of a weir in a TSCF located at the upstream end of the Proposed Bypass would 

require setting the invert of the Proposed Bypass at a substantially lower elevation 

downstream from the TSCF. This would substantially increase the footprint of the Proposed 

Bypass and required excavation, thereby increasing the overall project cost while reducing 

the area of adjacent land for other uses. 

3.2.4 Debris Management 

Debris management may also be easier at the upstream limit of the Proposed Bypass, as a 

single system could be used to manage all debris in the vicinity of the upstream end of the 

channel. Regardless of the location of the TSCF, consideration should be given to excluding 

large debris from entering the upstream end of the Proposed Bypass so as to minimize the 

need for debris management in the channel. 

A variety of approaches may be appropriate for debris management, including trash racks, 

debris booms, and/or piers in the adjacent reach of the Piscataquis River to deflect debris. A 

trash rack system with a 1-foot clear spacing located immediately upstream from the 

hydraulic entrance to the Proposed Bypass would provide an effective means for debris 

management, but might require substantial maintenance. A debris boom or piers to deflect 

debris might be less effective than a dedicated trash rack system but would likely require 

less maintenance. Existing piers in the Piscataquis River could potentially be used for debris 

management. 

The evaluation of the suitability of piers for debris management would need to evaluate flow 

routing over the Howland Dam during periods of high flow when large debris (e.g., whole 

trees) are likely in the adjacent reach of the Piscataquis River. 

3.2.5 Design Alternatives 

The conceptual TSCF design considers both "series" and "parallel" TSCF systems. A series 

TSCF refers herein to a system with a single route for upstream passing fish. A parallel 

TSFC system refers herein to a system with multiple routes for upstream passing fish, and 

may include routes without trapping facilities. The use of definitions based on upstream fish 

passage routes follows from the primary objectives of the Proposed Bypass—upstream fish 

passage, the recognized need for hydraulic conveyance in the Proposed Bypass, and the 

associated need for debris management. 

Both series and parallel TSCF systems would therefore consist of a trapping system 

handling a fraction of the total flow in the Proposed Bypass. The balance of the flow would 

be routed around the trapping facility through the TSCF conveyance channel with means to 

preclude upstream passage of all target species (series TSCF system) or allow upstream 

passage for a subset of target passage species (parallel TSCF system). 

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The TSCF conveyance channel barrier would necessarily consist of a hydraulic barrier. A 

screen system suitable for excluding juvenile target exclusion species across the Proposed 

Bypass would be subject to fouling by small debris, including aquatic vegetation and other 

detritus. A hydraulic barrier for full (series TSCF system) or partial exclusion (parallel TSCF 

system) of upstream fish passage is therefore considered as the only practical means to 

convey flow into the TSCF conveyance channel. A hydraulic barrier might consist of a free 

overfall (e.g., dam) or a reach with sustained high-speed flow and/or shallow depth under all 

conditions. The design of a hydraulic barrier to all upstream passing fish would need to 

evaluate the swimming ability of larger target species, including adult Atlantic salmon and 

northern pike. Little information is available on the swimming and leaping ability of northern 

pike, however, and a conservative design would therefore be necessary to exclude adult 

northern pike from passing the hydraulic barrier. It is assumed that a hydraulic barrier would 

block all but Atlantic salmon, and that all other target passage species would have to pass 

through the TSCF system. 

3.2.6 Parallel System 

A parallel TSCF system would be designed to provide upstream passage of adult Atlantic 

salmon through the TSCF conveyance channel based on their ability to leap barriers. A 

conceptual rendering of the parallel system is shown in Figure 1. Conceptual profile 

renderings of the trapping and sorting areas are shown in Figure 2. 

A potential benefit of a parallel system is decreased length of the primary conveyance reach 

of the Proposed Bypass and improved debris management. A partial barrier comprised of a 

hydraulic drop could reduce the overall length of the primary conveyance channel. For 

example, a four-foot high drop structure in a primary channel with an average slope of three 

percent would eliminate approximately 130 feet of primary channel. The smaller side 

channel through the TSCF trapping component could be set at the average channel slope, 

but would be smaller and therefore result in lower construction costs. Potential 

improvements to debris management could result from the ability to route debris past the 

TSCF trapping component without the need for trash racks and associated mechanical 

cleaning equipment across the primary conveyance channel. 

The design of a barrier intended to allow for upstream passage of Atlantic salmon would 

need to consider relevant fish passage criteria, including sufficient depth below the barrier. 

Location of the TSCF conveyance channel barrier along the upper reach of the bypass 

channel would likely be more practical for a parallel system relative to a series system given 

the substantially reduced leaping ability of the other fish species considered here. 

Partitioning of flows through a parallel system conveyance channel would need to consider 

seasonal, species-specific migration periods and costs associated with operation and 

maintenance of the trapping component. A potential benefit of the parallel system is that it 

would provide for upstream passage of Atlantic salmon during when total numbers of 

upstream passing fish do not warrant full-time operation of the trapping component. 

A critical design component of a parallel system would be assuring that the partial barrier is 

functional during periods of high flow when backwater conditions could potentially reduce 

the effectiveness of the partial barrier. 

A disadvantage of the parallel system is that it would not provide a means to trap all Atlantic 

salmon passing upstream through the Proposed Bypass. 

3.2.7 Series System 

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A series TSCF system would route all upstream passing fish through a trapping system. A 

benefit of this system is that it would provide means to trap all upstream passing fish. A 

conceptual rendering of the series system is shown in Figure 3. 

Location of a series TSCF conveyance channel barrier along the upper reach of the 

Proposed Bypass may be problematic due to the need to have a sufficient hydraulic drop to 

preclude passage by Atlantic salmon, and would therefore likely necessitate other measures 

to preclude passage, such as minimizing depths downstream from the barrier. Such 

measures would also need to consider minimizing potential impingement and/or impact 

hazards to downstream passing fish. 

3.2.8 Downstream Fish Passage 

The Proposed Bypass will provide downstream fish passage, and the design and operation 

of a TSCF must therefore consider potential impacts to downstream fish passage. 

Downstream passage of all fishes can be grossly considered based on the fraction of the 

flow through the Proposed Bypass relative to the total flow in the Piscataquis River. For 

example, if all flow is routed through the Proposed Bypass during periods of lower flow in 

the Piscataquis River, then all downstream passing fish would necessarily pass through the 

Proposed Bypass. 

Potential hazards to fish passing downstream through the Proposed Bypass include 

impingement on screening systems and impact after passing over the weir. Hazard 

mitigation can be accomplished through the use of appropriate design criteria (e.g., 

minimum flow speeds adjacent to screening systems). The use of a weir and velocity barrier 

for the series system described above poses a potential hazard to downstream migrating 

fish, as shallow depths immediately downstream from a weir could result in an impact 

hazard. This could be minimized by routing flows through the gate adjacent to the weir 

during periods of low flow. 

3.3 Operations and Maintenance 

Operational requirements at the TSCF may depend on factors including maximum holding 

times for trapped fish and/or delays at the TSCF and numbers of fish encountering the 

system. 

Maximum holding times for fish encountering the TSCF may be established based on 

regulatory requirements for minimizing disruptions to upstream migration and/or the holding 

capacity of the TSCF and the Proposed Bypass. The expressed intent to provide “safe, 

timely and effective passage of the target species” does not explicitly specify a maximum 

delay that might be imposed by the TSCF. 

Movement of fish through the TSCF is depicted in Figures 4 and 5 for the parallel and series 

systems, respectively. Maximum holding times based on regulatory requirements may vary 

seasonally and address only the target passage species or also include resident fish, such 

as white sucker. It is anticipated that the number of target passage species fish will increase 

over time following implementation of restoration projects in the Penobscot River watershed. 

An estimate of initial numbers of target passage species fish passing through the Proposed 

Bypass is presented here based upon potential alewife production in East Branch, 

Embeemee, and Upper Embeemee Lakes in the Piscataquis River. The production estimate 

for these three lakes is approximately 530,000 fish. Based on a 60-day migration period and 

a maximum daily passage rate of two-times the average passage rate, approximately 

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17,000 alewife per day would require handling at the TSCF to minimize delays to upstream 

passing these fish. 

Seasonal spawning migrations of white sucker would likely overlap with the alewife 

migration, thereby increasing the number of fish at the facility. While estimates of sucker 

numbers were not obtained for this study, the presence of multiple fish species complicate 

sorting operations. 

A preliminary analysis was performed to evaluate staffing needs at the TSCF during peak of 

an alewife run of 530,000 fish. Assuming 12 hours of sorting operations each day and a 

maximum daily passage rate of 17,000 fish, approximately 1,500 fish would need to be 

sorted each hour. 

Operation of a two-stage sorting would double the approximate number of fish to be 

handled. Given that the sorting work requires care to exclude target exclusion species, it is 

estimated that a staff of four would be required for this work. Based on a full labor rate of 

$30 per hour, the estimated cost for 30 days of peak migration sorting would be 

approximately $43,200. The estimated cost for a staff of two during the balance of the 

alewife migration is $21,600, resulting in a total estimated labor cost of $64,800 for the 60day 

alewife migration period. The cost of sorting for the projected alewife production in the 

Piscataquis River watershed (approximately 5,500,000 fish) at full productivity would likely 

be higher. Staffing of the TSCF would likely be required over the balance of the target 

passage species migration period, which extends to mid-April through mid-November for 


Assuming that a staff of one person could tend the trap for four hours each day from mid- 

April to the end of April and from July through mid-November, for a total of approximately 

150 days, the cost of this staffing would be approximately $18,000. 

The estimated operations costs presented here are for preliminary planning only, and would 

require revision based on the efficiency of sorting operations. These estimated costs do not 

include direct costs, such as transportation costs and maintenance of the TSCF. 

3.4 Eel Passage 

Dedicated passage facilities for American eel may be required for both the series and 

parallel systems due to the small size of upstream passing elver and to accommodate 

upstream movement of yellow-phase eels outside of typical migration windows. A variety of 

eel-specific passage systems that would not be suitable for upstream passage by the target 

exclusion species may be appropriate at this site. 

4 DISCUSSION AND CONCLUSIONS 

This evaluation presents information relevant to a TSCF on the Proposed Bypass adjacent 

to Howland Dam. The results of this evaluation suggest that total exclusion of the target 

exclusion species while allowing upstream passage of the target passage species cannot be 

achieved through the design of the Proposed Bypass, and that a dedicated TSCF would be 

required to trap, sort, and exclude the target exclusion species. 

Two schemes, series and parallel systems, are presented as general design configurations. 

General details are presented herein, but would need to be refined for the development of a 

final design. In addition to requiring a conservative design, successful operation of the TSCF 

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(i.e., total exclusion of the target exclusion species) would require thorough and ongoing 

oversight of facility operations. Based on the information and analyses presented herein, it is 

apparently unrealistic to expect a TSCF to provide total exclusion of the target exclusion 

species over a period of years. 

While apparently successful efforts have been made to modify the existing fishpass facilities 

at Howland Dam and at the West Enfield Dam to exclude upstream passage of northern 

pike, it is understood that these modifications prevent upstream passage of target passage 

species such as alewife and American shad. Such exclusionary measures are apparently 

not consistent with the overall restoration goals for the Penobscot River watershed. In 

addition, the efficacy of a TSCF for exclusion would be difficult to evaluate due to the 

potential for illegal, anthropogenic introduction of target exclusion species upstream from 

Howland Dam. 

Based on information and analyses performed for this study, incorporating a TSCF into the 

Proposed Bypass would have substantial impacts on the project objective of safe, timely 

and effective fish passage at Howland Dam. Additionally, a TSCF would apparently negate 

any benefits associated with the use of a nature-like fishway as the model for the Proposed 

Bypass due the need to trap and sort and otherwise hinder the free movement of migrating 

fishes at Howland Dam. 

5 SUMMARY 

The initial concept of a bypass channel on the Piscataquis River at Howland Dam was 

based upon successful European installations that provide simple, high capacity, and 

relatively low maintenance upstream fish passage. These European bypass channels are 

intentionally used to allow upstream and downstream passage of all species and all life 

stages. Inquiries have been made concerning potential means to exclude upstream passage 

of target exclusion species (i.e., northern pike and black crappy) through the Proposed 

Bypass and into the Piscataquis River watershed while providing safe, timely, and effective 

upstream and downstream passage of native diadromous fishes. 

The project team has evaluated several conceptual methods to prevent upstream passage 

of the target exclusion species, and determined that a conventional basket or chamber trap 

combined with manual sorting operations is the preferred procedure to attempt to achieve 

the objective of total exclusion. The following comments are noted for consideration of 

whether to use a trap and sort facility: 

a) There is no certainty that a trap and sort facility would be 100 percent effective. A 

successful combination of dam removal on the main stem of the Penobscot River and 

bypass channel at Howland dam could result in the restoration of millions of diadromous fish 

to the Piscataquis River watershed. 

b) A TSCF does not protect against intentional placement of non-native fish in the basin. 

c) A trap and sort facility would require significant operational and maintenance costs. 

d) A trap and sort facility would likely interfere with all upstream fish passage. 

Appendix A: Figures 

Figure 1 Conceptual Parallel TSCF System Plan 

Figure 2 Conceptual TSCF System Profiles 

Figure 3 Conceptual Series TSCF System Plan 

Figure 4 Conceptual Fish Handling in Parallel TSCF System 

Figure 5 Conceptual Fish Handling in Series TSCF System 

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Appendix B 

Outline for Preliminary Design of Proposed Howland Fish Bypass 

Final Draft July 12, 2007 

This outline will be used as the basis for a request for proposals for preliminary design of the 

Howland Fish Bypass. The RFP will contain introductory information from Sec. XI in the 

Settlement Agreement, which calls for a fish bypass system at Howland, provided it can be 

shown to achieve safe, timely and effective upstream and downstream passage of target 

species throughout their migratory periods and a range of flows including low flow periods. 

As described in the Settlement Agreement, use of an effective bypass system will allow for 

the existing Howland dam structure and impoundment to be substantially or entirely 

maintained. 

The RFP will also provide requisite design parameters that the resource agencies and/or 

PIN have identified to be necessary based on the Milone and MacBroom (MMI) report, 

Feasibility & Preliminary Environmental Assessment, Howland Dam, Howland, Maine, prior 

relicensing consultations on Howland, and other conditions associated with the site or needs 

of the target species. 

The preliminary design (along with the MMI report and other materials) will be part of the 

administrative record referenced in the Settlement Agreement, and will be used by the 

agencies and PIN as a basis for their commitment of support for the bypass prior to the time 

the Trust files its application for surrender of the license for the Howland hydro project. The 

Trust views the preliminary design as a critical planning step, which will be followed by 

continuing consultation and more detailed engineering work. Resource agencies and PIN 

will have an opportunity to review and comment on the results of the preliminary design 

study, and will be further consulted by the Trust on issues related to the bypass after the 

surrender application has been filed. 

The preliminary design will provide narrative information and engineering drawings, as is 

typically done when developing plans for conventional fish passage facilities during FERC 

licensing. The RFP for preliminary design will also request initial mathematical modeling 

(e.g., Computational Fluid Dynamics or CFD as recommended by Ben Rizzo of FWS) to 

describe future hydraulic conditions and predict fish movements in the area below the 

existing dam and powerhouse and within the bypass itself during the upstream and 

downstream migration period (as specified by the resource agencies – see for example, 

USFWS Sec. 18 Fishway Prescription for lower Penobscot River Hydro Projects, 1997). The 

modeling will take into account differential flow levels in the Penobscot and Piscataquis 

rivers, including those events when the high water levels in the Penobscot drown out the 

entrance to the bypass. Subsequent planning for the bypass (not covered in this RFP) will 

also include use of a physical model to better determine flow conditions and fine tune final 

construction plans to ensure safe, timely and effective passage of the target species. State 

and federal resource agencies and PIN will be consulted on specific requirements for both 

mathematical and physical models. 

The preliminary design will also evaluate the feasibility and costs (including operating costs) 

of incorporating provisions for trapping/sorting/counting of fish using the bypass. This 

includes measures to exclude upstream migration of northern pike and black crappie, both 

of which do not now exist above the Howland Dam, and are considered by Maine 

Department of Inland Fisheries and Wildlife to be undesirable, non-native invasive species. 

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Under the terms of the Settlement Agreement, the resource agencies are responsible for 

management activities such as trapping/sorting/trucking. 

As a separate effort, the Trust will use information from the preliminary design in developing 

its plans for long-term operation of the Howland fish bypass, including studies to evaluate 

the effectiveness of the system as described in the Settlement Agreement. The Trust will 

consult with the Town of Howland, resource agencies and PIN to reach agreement on 

responsibilities for day-to-day operation and maintenance of the bypass, including gates and 

control structures. (The state will need an agreement to ensure access to the bypass for 

carrying out routine fishery management activities, unless the state ultimately becomes 

owner of the facility.) The Trust will also consult with the Town of Howland, resource 

agencies and PIN to develop an annual schedule for operating the bypass. Information on 

annual and daily operations, responsible parties and contacts, and similar matters would be 

contained in a Standard Operating Procedure for the bypass that meets the approval of the 

resource agencies and PIN. 

The Trust will also consult with the Town and others to clarify roles and responsibilities in 

maintaining the Howland dam and lands surrounding the bypass. The Trust will involve the 

resource agencies and PIN in any discussions concerning recreational use of the bypass 

(e.g., fishing and boating) and abutting lands to ensure consistency with overall goals for 

fish restoration and management. The Trust plans to include the details on operation and 

maintenance of the bypass, dam and surrounding lands, including agreements with the 

Town and resource agencies/PIN in its license surrender filings with FERC and the state. 

Target Species 

Based on current agency/Tribal plans and overall goals of the Penobscot River Restoration 

Project, the Howland bypass should be designed to provide safe, timely and effective 

upstream and downstream passage for: 

Species upstream/downstream (lifestage) 

Atlantic salmon upstream (adult), downstream (adult, juv.) 

American shad upstream (adult), downstream (adult, juv.) 

Alewife upstream (adult), downstream (adult, juv.) 

Blueback herring upstream (adult), downstream (adult, juv.) 

American eel upstream (juv.), downstream (adult) 

Sea lamprey upstream (adult), downstream (juv.) 

Additional Design Criteria 

1. Slope: Based on the findings in the Milone and MacBroom report, the bypass slope 

should not exceed 3 % (they also modeled conditions with a 2.0 and 2.5 % slope). 

However, species-specific fish passage criteria (e.g., those contained in the Maine DOT’s 

Fish Passage Policy and Design Guide, 2nd ed., 2004) would be the basis for the actual 

design slope and placement of boulders and/or structures in the bypass. 

2. Operating Flows: The bypass should be designed to operate effectively whenever the 

flow in the Piscataquis River is at or below 9,000 cfs at Howland. This range of operable 

flows is consistent with what had been prescribed for fish passage during relicensing 

proceedings at Howland, and is proportionally equivalent to the 40,000 cfs that is being used 

for the design of the new fish lift at Milford on the Penobscot. (As an indication of distribution 

of flows between the river and bypass channel, the MMI report calculates that the bypass 

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channel would carry almost 1000 cfs when the river flows are approximately 8000 cfs. At 

summer low flow, almost all of the river discharge would go into the bypass.) 

3. Low flow channel – Relative to 2 above, passage during critically low flows will need to be 

addressed with a low flow channel. 

4. Water control structure – It is anticipated that the nature-like fish bypass will include a 

water management structure to maintain flows throughout the migratory run period. 

Outline of information to be requested in the RFP 

Narrative: 

Description of bypass fish channels that have been designed and/or constructed elsewhere 

in the world: brief discussion of concepts of fish bypasses; examples from elsewhere 

Description of Howland site: location - relationship to existing infrastructure (dam, 

powerhouse, roads & bridges, etc.); current/former ownership and uses of land, including 

any restrictions contained in deeds or regulatory orders; soil borings along channel (likely 

materials to be excavated, contamination); topography using one-foot contours 

Hydrology and hydraulic considerations: (reference previous HEC-RAS modeling by Milone 

and MacBroom) (supplement with tables to show data) river flows during passage season; 

high and low flow issues; range of operating flows (up to 9,000 cfs); relationship between 

bypass and river flows; range of water depths/widths/velocities in bypass during low, mean, 

and high flow events, including conditions when high flows in the Penobscot drown out the 

entrance to the bypass channel; relate hydraulic conditions to swimming abilities (design 

criteria) of target species; flooding and ice jams; results of additional modeling (computer 

derived), including analysis of flow field and velocity vectors below spillway near bypass 

entrance; need for control gate in upper end of bypass; assess the need for, and potential 

methods to enhance attraction flow under high flow conditions using powerhouse, flood 

gates, or other existing structures; future impoundment levels, head pond and tailwater 

elevations; hydraulic conditions at spillway and immediately below dam during downstream 

migration periods (to inform on whether downstream migrating fish will travel over the dam 

without injury or mortality, or if additional structures or modifications may be needed for 

downstream passage at the dam). 

Bypass design: layout (length, slope – not to exceed 3 % , width, depth, low flow channel, 

rock weirs/chevrons/resting pools, rip-rap side slopes, entrance and exit relative to existing 

spillway, gates and attraction flows); use of surrounding land; public safety issues 

Construction: construction equipment access and road grading; removal of existing turbines, 

flashboards, etc.; use of powerhouse and adjacent gates for attraction flow purposes; 

bypass materials and construction methods (earthen cuts and fills, boulders for weirs and 

rip-rap); need for modifying ledge material below bypass entrance to enhance fish 

movement; erosion/sedimentation controls; disposal of excavated materials; removal of 

temporary access and revegetation of banks areas; schedule (start, finish, work during 

winter, expected milestones); mitigation for affected infrastructure (existing storm drains, 

boat ramp, etc.); duration of construction; costs 

Also information (including itemized cost estimates) for: 

- mobilization and demobilization 

- installation and removal or restoration of construction access roads 

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- methods and location for diversion of water 

- erosion and sedimentation control 

- excavation, removal and disposal, at an approved off-site location, of excavated materials 

- extension of storm drainage facilities 

- removal of submerged upstream cofferdam materials left from previous projects 

- removal of piers and other submerged remains of previous developments 

- mitigative measures that may are found necessary upon inspection of the lowered 

reservoir area 

- water control structure 

- final design planning 

- construction management 

- permitting 

- contingencies 

Operation & maintenance: anticipated schedule and costs of routine operations and 

maintenance of the bypass channel, control structure and other design features 

Preliminary engineering design drawings: 

The preliminary design drawings will include the existing conditions plans (preferably 50scale 

plans or smaller scale), plan view sheets (with centerline and station numbers) of 

channel and cross vane structures, channel profile (tied into station numbers), cross 

sections of the channel (at the cross vane locations and some areas between cross vanes) 

and overtop floodplain, and details of the water control structure, stone sizes and 

composition, and sequence of construction notes. The channel design should take into 

account not only low flow conditions, but how weaker-swimming fishes (e.g., juvenile eels) 

may be accommodated in the design (e.g., near shore rock or log structures) during at least 

normal flows. Any needs for floodplain and channel bank (re)vegetation should be included 

as part of a planting plan in the preliminary plan set. Lastly, the consultant should be 

encouraged to include any public safety measures in the plans, as needed. 

The consultant will be expected to provide all information to develop and complete the 

preliminary design plans. The plans will likely consist of six or more sheets (plans should be 

annotated with symbol legend and key design parameters – including operating flows, water 

surface elevations, and velocities): 

1. Existing conditions plan depicting topography and bathymetry of the project site area, as 

well as head pond and tailwater surface elevations, flagged wetland boundaries, existing 

infrastructure, soil boring locations, and other natural or man-made features potentially 

affecting or affected by project design. 

2. Scaled plan view of the preferred design alternative, depicting dimensions, expected 

channel geometry/sinuosity, channel grade slope and bank slopes, rock material, instream 

grade control structures, water control structure, and other important features. 

3. Profile and cross-section views of bypass channel and structures, including low flow 

channel, overbank floodplain grades, and expected water levels in bypass during low, 

normal and high operating flows and flood flows. The cross sections of cross weir structures 

will also be provided. 

Details of temporary water diversion and/or water control, channel and rock materials (sizes 

and composition), water control structure, entranceway (in relation to existing dam and 

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powerhouse), rock weir/chevron/resting pools, channel banks, and sequence of 

construction. 

Appendix C 

Simplified spatial and temporal overlap of diadromous fishes in the Penobscot River 

ecosystem, where arrows represent peak activity periods. 

In many cases, movement patterns may be quite complex: for example, adult 

salmon may enter the river as early as April with a peak in June, dwindling off at the 

end of June and then another group of adults may move in beginning in August with 

a peak in September. Shown are rainbow smelt (Osmerus mordax), American eel 

(Anguilla rostrata), alewife (Alosa pseudoharengus), sea lamprey (Petromyzon 

marinus), blueback herring (Alosa aestivalis), American shad (Alosa sapidissima), 

and Atlantic salmon (Salmo salar). Not shown are shortnose sturgeon (Acipenser 

brevirostrum), Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus), brook trout 

(Salvelinus fontinalis), Atlantic tomcod (Microgadus tomcod), and striped bass 

(Morone saxatilis), which would have spawned in the lower Penobscot River, below 

the first set of falls in Milford, Maine. YOY = young-of-year. Figure modified from 

Saunders et al. (2006) and information in Collette and Klein-MacPhee (2002). 

(Information copied from page 63 of the Strategic Plan for the Restoration of 

Diadromous Fishes to the Penobscot River prepared by Maine Department of 

Marine Resources and the Maine Department of Inland Fisheries and Wildlife [March 

2008]) 

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Appendix B: A handout summarizing Stantec’s evaluation 

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Appendix C: The pattern of introduction and dispersal in lakes from the 

discovery record graphically illustrated in a map time series 

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Appendix D: Invasive species response and the Eastern Brook Trout joint 

Venture (EBTJV) 

The Eastern Brook Trout Joint Venture: Fish Habitat Partnership (EBTJV) is a 

National Fish Habitat Action Plan partnership of state and federal agencies, 

nongovernmental organizations, and academic institutions. The EBTJV conducted a 

comprehensive assessment of the status of and threats to brook trout populations 

throughout their entire eastern United States range (Maine to Georgia) in 2005 

(Hudy et al. 2005). It revealed wild brook trout populations in the eastern United 

States are impaired. Intact stream populations of brook trout populations exist in only 

5% of the watersheds assessed. Wild stream populations of brook trout have 

vanished or are greatly reduced in nearly half of the watersheds. The vast majority of 

historically occupied large rivers no longer support self-reproducing populations of 

brook trout. 

Across the entire eastern brook trout range, the top five perturbations for streamdwelling 

brook trout populations were high water temperature, agriculture, riparian 

condition, non-native fish species, and urbanization. Non-native fish species were 

considered the greatest threats to lake populations. Findings from the range-wide 

status and threats assessment were used to develop a unified vision, as well as 

goals, key priorities, and strategies for the Joint Venture. 

The EBTJV’s Conservation Strategy (EBTJV 2008) is a goal-oriented, sciencebased, 

action plan that explicitly states Joint Venture partner goals, presents 

guidance for decision-making, and provides methods for evaluating success. The 

fundamental framework of the Conservation Strategy is comprised of three distinct 

components: (1) vision; (2) principal goals and (3) key priorities. Because of the 

large geographic distribution of brook trout in the eastern United States, the EBTJV 

conservation strategy is organized into three primary levels of distinction: rangewide, 

regional, and state-level. 

The range-wide vision of the EBTJV is to ensure “healthy, fishable brook trout 

populations throughout their historic eastern United States range.” Key priorities 

serve as the framework for the development of state-level brook trout conservation 

action plans. The following key priorities were established to meet the principal 

goals of the EBTJV: 

1. Protect brook trout populations across the eastern United States. 

2. Restore brook trout populations where original habitat conditions exist and 

where habitats can be restored. 

3. Monitor and evaluate brook trout population responses to habitat 

protection, enhancement and restoration projects. 

4. Complete brook trout distribution and quantitative status assessments. 

5. Increase recreational fishing opportunities for wild brook trout. 

The state level is where the vast amount of brook trout conservation efforts occur. 

The EBTJV believes that efforts to improve the status of brook trout should begin by 

protecting “the best of the best” habitat that supports existing healthy, stable 

PRFP Page 297

populations. Although each member state developed a unique plan, common goals, 

objectives, and strategies were evident. With respect to invasive species concerns, 

commonalities among state plans for the EBTJV Conservation Strategy is summed 

by: 

• Prevent the spread of invasive species into brook trout habitat. 

a. Develop EBTJV-produced educational pamphlets that highlight 

state-level, regional, and range-wide threats from invasive species. 

Update annually. 

b. Develop lists of invasives with state or federal agencies responsible 

for permitting aquaculture operators or distributors. 

c. Eradicate invasive species from brook trout habitat where feasible. 

(EBTJV 2008) 

Maine’s Plan for the EBTJV 

The Joint Venture is comprised of 17 states within the historical range of brook trout 

in the eastern United States. Each state was asked to produce a state-level brook 

trout conservation plan consistent with the vision of the EBTJV framed around the 

five key priorities. Maine’s Plan was drafted in 2006 and accepted by the EBTJV 

Conservation Strategy/Habitat Subcommittee that same year. 

Maine’s wild brook trout populations are concentrated in the interior highlands of the 

state, such as the Piscataquis River drainage. In 2005, the EBTJV status 

assessment found that Maine possessed almost 150 subwatersheds containing 

intact stream-dwelling brook trout populations. Survey efforts since then have 

documented approximately 200 additional subwatersheds with intact stream dwelling 

brook trout populations and 55% (18/33) of the Piscataquis River’s subwatersheds 

maintain healthy wild brook trout populations (Figure 1). Intact brook trout 

populations in lakes are confined exclusively to the northern states of Maine, New 

Hampshire, New York, and Vermont. In Maine, brook trout lakes in 323 

subwatersheds have severely reduced status. 

Maine identified invasive species issues as serious concerns for both lentic and lotic 

populations of brook trout (Hudy et al. 2005). Hence, strategies for mitigating the 

effects of invasive species are featured prominently in Maine’s Plan for the 

Conservation Strategy of the EBTJV (EBTJV 2008) and are listed below. 

PRIORITY 1: Assessment 

1.3 Maximize the contribution of wild brook trout stocks to the fishery. 

Strategy 1.3.5. Prevent, eradicate or control the detrimental effects caused by 

the intrusion of non-native aquatic species into brook trout habitats. 

PRIORITY 2: Habitat Protection 

2.1 Identify degraded stream habitats and prioritize sites for restoration efforts 

PRFP Page 298

Strategy 2.1.3. Prevent the intrusion of non-native aquatic species into 

previously uncolonized habitats where natural landform provides 

strategic opportunities for optimal or selective barrier placement. 

2.3 Permanently protect critical habitats. 

Strategy 2.3.1. Establish collaborative partnerships with State, Federal, Tribal 

and private entities for the permanent conservation of critical wild 

brook trout habitats and refuges. 

PRIORITY 3: Outreach 

3.2 Foster public/private collaborative stewardship of brook trout resources 

Strategy 3.2.2. Continue public education efforts highlighting the permanent 

ecological repercussions associated with illegal fish stockings. 

Figure 1. EBTJV status of wild brook trout populations in the Piscataquis River drainage. 

Dark green areas denote subwatersheds with 50% or greater occupied habitat and lighter 

green subwatersheds signify less than 50% habitat occupied by wild brook trout. Gray areas 

signify subwatersheds where wild brook trout but quantitative assessment is not complete. 

PRFP Page 299

Appendix K – Northern Pike Movement Barrier Risk Assessment Survey 

PRFP Page 300

MAINE DEPARTMENT OF 

MARINE RESOURCES 

BANGOR, MAINE 

NORTHERN PIKE MOVEMENT BARRIER RISK 

ASSESSMENT SURVEY 

JULY 2009 

Prepared by: 

1

MAINE DEPARTMENT OF MARINE RESOURCES 

BANGOR, MAINE 

NORTHERN PIKE MOVEMENT BARRIER RISK ASSESSMENT SURVEY 

JULY 2009 

Prepared by:


BANGOR, MAINE 


TABLE OF CONTENTS 

1.0 INTRODUCTION .............................................................................................................. 1 

2.0 DESCRIPTION OF THE STUDY AREA ......................................................................... 2 

2.1 East Branch Lake .................................................................................................... 2 

2.2 Wangan and Sanborn Brooks.................................................................................. 2 

3.0 METHODS ......................................................................................................................... 4 

4.0 RESULTS ........................................................................................................................... 5 

4.1 East Branch Lake .................................................................................................... 6 

4.1.1 Seboeis Stream Outlet ................................................................................. 6 

4.1.2 Nollesemic Outlet ..................................................................................... 11 

4.1.3 Wangan and Sanborn Brooks.................................................................... 14 

5.0 DISCUSSION ................................................................................................................... 17 

5.1 East Branch Lake .................................................................................................. 17 

5.2 Wangan and Sanborn Brooks................................................................................ 18 

6.0 LITERATURE CITED ..................................................................................................... 19 

LIST OF FIGURES 

Figure 1: East Branch Lake Showing Both the North and South Outlet Streams ...................2 

Figure 2: Headwaters of Wangan and Sanborn Brooks ..........................................................3 

Figure 3: Horizontal Schematic View of South Outlet (East Branch Seboeis Stream) 

of East Branch Lake, Maine, May 29, 2009 at 18.5 cfs ...........................................9 

Figure 4: Water and Channel Elevations, South Outlet of East Branch Lake, Maine 

(Cross-Sectional View Looking Upstream) ...........................................................10 

Figure 5: Water and Channel Elevations, North Outlet of East Branch Lake, Maine 

(Cross-Sectional View Looking Upstream) ...........................................................13 

Figure 6: Location of Beaver Flowage Relative to Sanborn Brook, Wangan Brook 

and Governing Topographic Features (Red Line Indicates Partial GPS 

Track During Survey) ............................................................................................15 

i

Table of Contents (Cont’d) 

LIST OF PHOTOS 

Photo 1: East Branch Seboeis Stream Approximately 100 Meters Downstream from 

East Branch Lake Outlet ..........................................................................................6 

Photo 2: View of South Outlet of East Branch Lake, Looking Upstream .............................7 

Photo 3: View Looking Downstream of South Outlet of East Branch Lake Showing 

Field Stone Walls and Cribwork (left) and Hydraulic Control of East 

Branch Lake (right) ..................................................................................................7 

Photo 4: View Looking Upstream at Cross-Section on Un-named North Outlet 

Stream Connecting East Branch Lake to Nollesemic Lake Where the 

Stream Channel is Well-Defined ...........................................................................11 

Photo 5: View Looking Downstream on Un-named North Outlet Stream 

Connecting East Branch Lake to Nollesemic Lake Where the Stream 

Channel Becomes Braided and Choked with Woody Debris ................................11 

Photo 6: View Looking Northwesterly Toward Beaver Flowage from Upstream- 

Most Extremity of Depression that Forms an Ephemeral Tributary to 

Sanborn Brook. ......................................................................................................16 

LIST OF APPENDICES 

Appendix 1: Survey of Natural Barriers in Headwater of Wangan Brook 

\\falcon\jobs\287\008\Docs\002 - Northern Pike Movement Barrier Risk Assessment Survey 07-27-09.doc 

ii


BANGOR, MAINE 


1.0 INTRODUCTION 

In recent years non-indigenous fish species have become widespread throughout Maine, 

in some cases by deliberate introductions, and in other cases due to colonization from an 

expanding local population. In some cases, there have been documented impacts to native 

species, such as brook trout, and other non-game species resulting from these invasions (Boucher 

and Bonney, 2004; Gallagher, 2004). 

Northern pike (Esox lucius) were illegally introduced into the Belgrade Chain of Lakes in 

the 1970s, and are now present in the Kennebec, Androscoggin, and coastal river drainages 

(Maine DIFW, http://www.maine.gov/ifw/fishing/illegal_stocking.htm). In the Penobscot 

watershed, a northern pike population is established in Pushaw Lake, a tributary lake near 

Bangor. 

Northern pike are believed to be presently confined to the Pushaw Stream subwatershed 

in the Penobscot drainage. Routine fishery monitoring and also recent electrofishing surveys of 

Pushaw Stream and the Penobscot River have not detected northern pike at other locations 

(Yoder, et al. 2005; Kleinschmidt Associates, 2009). However, there is no barrier preventing 

volitional access from the Pushaw drainage to the mainstem Penobscot River. Should the 

species ever become established in the Piscataquis River drainage, two tributary streams with 

headwaters in a breached divide between the Piscataquis and West Branch Penobscot drainages 

potentially could serve as a thoroughfare allowing northern pike to invade the West Branch. The 

two sites of interest are: Wangan Brook (southern-flowing inlet to Upper Ebemee Lake) in 

Piscataquis County and East Branch Lake which connects the East Branch Seboies Stream to 

Nollesemic Lake in Penobscot County. 

The goal of this survey is to provide an analysis of the potential for these two streams to 

provide access to the West Branch for northern pike, based on surveyed stream channel 

conditions. 

1

2.0 DESCRIPTION OF THE STUDY AREA 

2.1 

East Branch Lake 

East Branch Lake lies within T3R9 NWP, and is the headwater of the East Branch 

Seboeis Stream, which exits the lake along the southern shoreline (Figure 1), then flows 

south to the confluence with the Piscataquis River near Howland, Maine. The majority of 

stream flow exits East Branch Lake via this outlet. Another small, un-named brook exits 

the northeast corner of the lake and flows north to Nollesemic Lake. Nollesemic Lake in 

turn discharges to Nollesemic Stream and ultimately connects to the West Branch 

Penobscot near Millinocket, Maine. 

Figure 1: East Branch Lake Showing Both the North and South Outlet Streams 

2.2 

Wangan and Sanborn Brooks 

Wangan Brook originates on the east slope of an esker in T8R10 WELS, and 

descends easterly to a forested wetland valley oriented north/south, where it turns south 

as a second-order stream, and eventually confluences with the East Branch Pleasant River 

2

at Upper Ebeemee Lake. The Pleasant River enters the Piscataquis River near Milo, 

Maine. Sanborn Brook originates from a tributary westerly of Sanborn Pond which is 

located in the same esker valley slightly north of Wangan Brook (Figure 2). Sanborn 

Brook flows north to Upper Jo-Mary Lake, and eventually drains to Pemadumcook Lake 

which is a flowage of the West Branch Penobscot including North Twin and South Twin 

lakes. The terrain separating these two small streams is comprised of a low-relief, 

forested wetland and mixed conifer forest, and a complex of alder thicket and beaver 

ponds. A short trough depression has formed a small perennial stream that exits an 

abandoned beaver dam southward to a connection with Wangan Brook. Another 

depression extends between a bend in Sanborn Brook southwesterly toward Wangan 

Brook that could convey water at high flows. 

Figure 2: Headwaters of Wangan and Sanborn Brooks 

(Red dotted line indicates pathway of trough that potentially could connect both 

watersheds) 

3

3.0 METHODS 

Both streams were surveyed the week of May 25, 2009. Maine DIFW provided 

invaluable guidance on access and locations, including GPS waypoints, especially for the 

Wangan Brook site (T. Obrey, and Richard Dill, Maine DIFW, personal communication). 

Wangan Brook was reinvestigated a second time on July 8, 2009 following an extended period of 

high rainfall which increased water levels through the study site. 

At each site, the most limiting passage point for migrating fish in the thoroughfare area 

was located and geo-referenced. Factors such as stream slope, water depth, velocity, presence of 

any physical obstruction (both vertical and horizontal) were collectively considered to evaluate 

each limiting passage site. Although the survey occurred in late May, northern pike could be 

active immediately after ice-out when water levels are significantly higher (and thus hydraulic 

conditions different). Thus the seasonal high water elevation at each site was also identified and 

surveyed. Bankfull indicators such as changes in vegetation, leaf and substrate disturbance and 

bank erosion were collectively used to approximate the elevation of high water. 

Each site was geo-referenced with a Trimble model Geo XH GPS unit, and a cross- 

section transect established. Transect data included bed profile elevations, water surface 

elevations (WSEL's) at the existing stream flow and at estimated bankfull. Lateral survey 

boundaries of each transect were defined by head- and tailpins established above the crest of 

each bank. Headpins were located along the right bank (looking downstream). Pins were field- 

blazed and semi-permanently fixed with either rebar or by using a large tree or other fixed object 

and then field blazed with flagging and/or survey paint. 

A 300-ft fiberglass survey tape was secured between headpin and tailpin at each transect. 

Elevation and edge of water were recorded at intervals (verticals) along the tape. Verticals were 

established wherever an observable change in profile occurred and/or at locations of special 

interest such as hydraulic controls. In the case of cribwork, beaver dams etc., water and object 

elevations were gathered across both the crest and toe of the obstruction. Bed and water surface 

elevations were surveyed to the nearest 0.01-ft elevation using a surveying level and standard 

surveying techniques. Each site was also photographed and schematically sketched. 

4

Discharge through the study area is unregulated, and therefore subject to precipitation 

and climatic events. A staff gage was semi-permanently installed in the vicinity of each study 

site to verify that discharge remained adequately stable during hydraulic measurements and also 

to potentially serve as reference should future site visits occur at other discharge levels. Stage 

(water height) was recorded at the beginning and end of each survey. 

A discharge measurement transect was located in the vicinity of the study area in a 

location featuring a relatively flat stream bottom with non-turbulent flow. Velocity was 

measured at intervals along the transect to the nearest 0.1-ft/s , using a calibrated Marsh- 

McBirney Model 2000 Flowmate electronic current meter attached to a top-setting wading rod. 

In water less than 2.5-ft deep, mean-column-velocity was measured at 0.6 of the depth. In water 

greater than 2.5-ft deep, mean-column-velocity was taken as the average of the velocities 

measured at 0.2 and 0.8 of the depth. Each point velocity measurement used on a given vertical 

was the mean of a series of 20-second time-averaged readings. 

5

4.0 RESULTS 

4.1 


4.1.1 

Seboeis Stream Outlet 

The East Branch Seboeis Stream outlet of East Branch Lake is the major 

outlet of the lake and approximately 16 ft wide; the stream below the outlet 

widens to approximately 25 ft, and features a channel sufficiently deep and 

unobstructed for northern pike to readily ascend the stream. The stream channel 

is well-defined and provides instream and riparian cover, including resting pools 

and channels suitable for adult fish movement, resting and foraging (Photo 1). 

Photo 1: East Branch Seboeis Stream Approximately 100 Meters Downstream from 

East Branch Lake Outlet 

The stream exits the lake via a man-modified notch with fieldstone walls 

and cribwork that appears to have once been dammed (Photos 2 and 3). The 

existing hydraulic control for East Branch Lake lies just upstream from the outlet 

at a slightly higher elevation than the outlet. 

6

Photo 2: View of South Outlet of East Branch Lake, Looking Upstream 

Photo 3: View Looking Downstream of South Outlet of East Branch Lake Showing 

Field Stone Walls and Cribwork (left) and Hydraulic Control of East Branch 

Lake (right) 

Stream flow was gauged as 18.5 cfs. At that discharge water descends 

from the lake hydraulic control through turbulent rapids to the cribwork, where it 

cascades over the log crest to a second shallow riffle which descends to a wide 

pool/run. A fish ascending from the pool toward the crib work would experience 

riffle depths of 9-14 inches, and maximum velocities of 5 ft/sec prior to arriving 

at the crib work. The elevation difference between the crib toe to crib crest was 

0.4 ft (approximately 5 inches); at 18.5 cfs the net hydraulic head difference was 

0.6 ft (approximately 7 inches) (Figures 3 and 4). Upstream from the cribwork, 

the lake outlet hydraulic control elevation is 0.4 inches higher than the crib crest; 

and under the field conditions observed, the water elevation (97.7 ft. survey 

7

elevation) difference from the crib to the lake hydraulic control was 2.2 ft. 

However, the spring bankfull elevation line in the stream at a point downstream 

from the cribbing corresponded to an elevation 0f 97.8 ft, which is slightly higher 

than that of the June lake elevation, and also 1.9 ft higher in elevation than the 

outlet hydraulic control. This suggests that under peak spring run-off all outlet 

structures and the lake hydraulic control at this site are submerged. The duration 

and exact timing of this condition is currently undocumented. 

8

Lake el. 97.7 outlet hydraulic control el. 95.9 crib top water el. 96.4 el. Spring high water 97.8 

EAST BRANCH LAKE 

outflow 

9 

Water elevation below crib 95.8 

Top of crib el.95.5 Bottom of crib el. 95.1(typical) 

Figure 3: Horizontal Schematic View of South Outlet (East Branch Seboeis Stream) of East Branch Lake, Maine, May 29, 2009 

at 18.5 cfs 

(Not drawn to scale; features exaggerated for clarity)

Figure 4: Water and Channel Elevations, South Outlet of East Branch Lake, Maine (Cross-Sectional View Looking Upstream) 

10

4.1.2 

Nollesemic Outlet 

The un-named north outlet to Nollesemic Lake is a much smaller stream 

than the south outlet. It exits the lake via a wetland complex, and passes through 

upland forest, where the channel becomes highly braided and choked with woody 

debris and blow down. A defined stream channel briefly appears about 100 

meters upstream of the road that passes north of the lake; this channel resumes 

becoming blocked by braids and woody debris about another 100 meters 

downstream from the road (Photos 4 and 5). 

Photo 4: View Looking Upstream at Cross-Section on Un-named North Outlet Stream 

Connecting East Branch Lake to Nollesemic Lake Where the Stream 

Channel is Well-Defined 

Photo 5: View Looking Downstream on Un-named North Outlet Stream Connecting 

East Branch Lake to Nollesemic Lake Where the Stream Channel Becomes 

Braided and Choked with Woody Debris 

11

A portion of the stream passes to the east of this watercourse, through an 

unwadable, muddy lowland swale with no defined channel. Fish exiting the lake 

via this outlet would descend in elevation but encounter dense thickets of brush 

and downed trees and shallow, braided stream channels where flow is dispersed 

and to some extent passes interstitially through substrate, sediment, rootwads, and 

brush incapable of passing adult sized fish. The areas covered by shallow braids, 

marsh and blow down did not lend themselves to surveying. The well-defined 

stream channel in the vicinity of the road channel was surveyed at a natural 

constriction featuring a concentration of cobble-sized rocks that could limit 

passage at least at lower flows (Figure 5). 

12

Figure 5: Water and Channel Elevations, North Outlet of East Branch Lake, Maine (Cross-Sectional View Looking Upstream) 

13

4.1.3 

Wangan and Sanborn brooks are separated by a low-relief height-of-land 

traversed for approximately a 500-700 ft. distance by a narrow, low lying depression 

through the forested esker valley. The depression extends from a sharp bend in Sanborn 

Brook westerly to the vicinity of a beaver flowage which is a tributary to Wangan 

Brook. The beaver dam emits discharge down a short connector stream channel to 

Wangan Brook. 

On the date of the May site visit, Wangan Brook flow was gaged at 3.3 cfs and 

flow in the connector channel was 1.5 cfs. During the July site visit, Wangan Brook 

was not gaged, but estimated to be discharging about 10-15 cfs, and showed evidence of 

having recently receded from slightly over its banks. The reach of Wangan Brook at the 

toe of the esker that curves near the beaver pond shows evidence of stream evulsions; 

an abandoned channel of the brook appears to have received overflow that potentially 

funneled into the lower end of the beaver flowage under extremely high runoff 

conditions. 


Most of the connector channel is trapezoidal-shaped, and comprised of 

vegetated, earthen banks and fine substrates. A staff gage in the connector stream 

indicated that the water level had risen 2 inches relative to May water levels in response 

to increased July outflow from the beaver flowage. The beaver pond water elevation 

had risen by approximately one foot. 

At the point of confluence, both Wangan Brook and the beaver flowage 

connector channels are sufficiently deep, wide and slow-flowing enough to 

accommodate volitional passage of adult fish, including northern pike under the 

observed flow conditions. Two barriers in the connector channel were surveyed in May 

to determine if pike could gain access to the beaver pond (Appendix 1). Although the 

beaver flowage is part of the Wangan Brook watershed, it is perched close to a shallow 

watershed divide. Thus the surrounding topography was revisited in July (after heavy 

rains increased surface runoff) to empirically observe if low lying areas between the 

14

eaver flowage and Sanborn Stream provide a hydraulic connection suitable for fish 

passage. 

The beaver flowage water elevation is presently controlled by the breached 

outlet of the dam and is the part of the Wangan Brook drainage that comes closest to the 

Sanborn watershed (Figure 6). All low-lying areas that might conduct water between 

the beaver flowage and Sanborn Brook throughout this area were walked in July 

immediately following an extended period of heavy rains that temporarily resulted in 

near-spring stream runoff conditions. Several small ephemeral tributaries were 

observed to flow into the Sanborn drainage from the direction of the beaver flowage, 

but were confirmed to have no direct hydraulic connection to the beaver flowage. A 

slight height of land between the drainages was observed that divides the existing 

beaver flowage from the nearest stream head by approximately 250 ft. (Photo 6). It is 

apparent by examination of undisturbed leaf litter, vegetation and forest duff across this 

height of land that this watershed divide has not recently been subject to inundation, and 

thus is not a connection that migrating fish can utilize to cross between watersheds. 

Figure 6: Location of Beaver Flowage Relative to Sanborn Brook, Wangan Brook and 

Governing Topographic Features (Red Line Indicates Partial GPS Track During 

Survey) 

15

Photo 6: View Looking Northwesterly Toward Beaver Flowage from Upstream-Most 

Extremity of Depression that Forms an Ephemeral Tributary to Sanborn Brook. 

Beaver flowage is approximately 250 ft distant (can be seen as the clearing in the distance). 

Elevation of divide appears to be approximately 2-3 ft. higher than pool elevation of 

beaver flowage. 

16

5.0 DISCUSSION 

5.1 

Under the existing conditions, it appears that it is theoretically possible for 

northern pike to access the West Branch Penobscot drainage by way of East Branch 

Lake. Pike established in the Piscataquis/Seboeis drainage would be able to ascend East 

Branch Seboeis Stream to the outlet of the lake where the crib work of an abandoned dam 

forms a partial barrier under low flow conditions. Under flow conditions found in this 

survey, a pike would need to swim upstream against the riffle flow, then leap a 0.4 ft 

hydraulic jump at the crib work. Bell (1990) gives the maximum darting speed of a 14inch 

pike as 4 ft/sec., which is less than the observed velocity of the riffle immediately 

below the lake outlet. This suggests that most pike would have a difficult time ascending 

the riffle to the cribbing. At lower outflows, the velocity may be reduced, but channel 

depth would also be reduced, which may also inhibit the ability of a pike to ascend the 

riffle and complete a leap over the cribbing. However under spring run-off conditions 

this barrier may be sufficiently submerged to briefly enable free swim passage upstream 

to the lake. 


Northern pike from East Branch Lake would next need to traverse downstream 

via the unnamed stream to the north to enter the West Branch drainage via Nollesemic 

Lake. This outlet stream appears to be impassible for adult-sized pike due to the 

preponderance of wetland, blow down thickets and shallow braids, which limits 

downstream passage to only shallow and interstitial channel routes. However it is 

possible that young of year or juveniles produced by a breeding population of East 

Branch Lake pike could be sufficiently small to potentially pass downstream through 

these obstacles and thus colonize Nollesemic Lake. 

We conclude that if pike were to become established in East Branch Lake, there is 

potential for the species to eventually colonize their way downstream toward the West 

Branch if juvenile fish traverse the un-named brook. Although the probability of this 

occurring appears relatively low, it cannot be ruled out. Therefore, if a future fish barrier 

solution is deemed justified, strategic options include construction of a barrier at a 

17

location that would prevent fish from ascending to East Branch Lake from the Seboeis 

Stream, or alternatively, closing the outlet to the Nollesemic drainage with a dike. 

5.2 


Fish movement access to the Sanborn Brook watershed from Wangan Brook does 

not currently exist due to the low divide separating the beaver flowage in the Wangan 

Brook watershed from ephemeral stream channels that are tributaries to Sanborn Brook. 

Although these channels are not connected to the beaver flowage, they begin to 

form just a few hundred feet away from the flowage just beyond a low-relief divide. The 

close proximity of this divide to the beaver dam in low-gradient topography means that 

the integrity of this barrier may be potentially subject to any changing physical condition 

of the beaver dam. The condition, size and volume of beaver flowages can be very 

ephemeral. Likewise, the evulsive nature of the Wangan Brook channel where it passes 

near the beaver dam means that the channel may migrate either away from, or toward the 

beaver flowage over time. Under a scenario where the dam was re-built by beaver, a 

higher flowage level may be restored that is nearer in elevation to that of the divide. 

There is evidence that at high flow an existing side channel of Wangan Brook could 

theoretically fill a restored beaver flowage to the point where the existing low-profile 

divide might be breached. Any northern pike inhabiting the beaver flowage could, under 

those very specific set of hydraulic conditions (that may persist only briefly) escape to the 

Sanborn drainage. The probability of this occurring appears extremely low, however it 

may be advisable to periodically re-inspect this site to confirm that the status of the 

beaver flowage relative to Wangan Brook and the divide has not changed. 

18

6.0 LITERATURE CITED 

Bell, M.C. 1990. Fisheries handbook of engineering requirements and biological criteria. Fish 

passage development and evaluation program. Corps of Engineers, N. Pac. Div., 

Portland, OR. 

Boucher, D.P. and F.R. Bonney. 2004. Rapid River fishery management. American Fisheries 

Society, Atlantic International Chapter Annual Meeting. Lake Morey, Vermont. 

September 2004. 

Gallagher, M. 2004. Comparing Maine lake and stream fish assemblages as a function of 

watershed condition. American Fisheries Society, Atlantic International Chapter Annual 

Meeting. Lake Morey, Vermont. September 2004. 

Kleinschmidt Associates. 2009. Penobscot River fish assemblage survey interim report. 

January, 2009. NOAA Fisheries, Woods Hole, MA. 

Yoder, C.O., B.H. Kulik and J.M. Audet. 2005. Maine rivers fish assemblage assessment: 

Interim Report II. Penobscot River & tributaries: 2004. Midwest Biodiversity Institute 

Center for Applied Bioassessment & Biocriteria, Columbus, OH 43221; Kleinschmidt 

Associates, Pittsfield, ME. 94 pp. 

19

APPENDIX 1 

SURVEY OF NATURAL BARRIERS IN HEADWATER OF WANGAN BROOK 

A boulder and cobble riffle constriction was observed at approximately the midpoint of 

the beaver flowage connector channel that, at low flow, is the first potential barrier to a pike- 

sized fish moving upstream from Wangan Brook (Photos A-1 and A-2). 

Photo A-1: View of Typical Channel Connecting Beaver Flowage to Wangan Brook 

Photo A-2: Instream Passage Constriction Between Beaver Flowage and Wangan Brook. 

Orange Blazing Indicates Transect Location (view looking upstream) 

A-1

Transect W-1 was located at this constriction, and was configured to transect both the 

connection channel and also Wangan Brook above the confluence (Figure A-1). Upstream 

passage for adult or juvenile northern pike would be restricted under these flow conditions; 

however, the bankfull elevation indicates that under peak spring run-off conditions, this riffle 

would be submerged (Figure A-2). Given the relatively low gradient of this reach, it is unlikely 

that velocities at peak run-off would be limiting for upstream movements, in which case, this 

would cease to be an upstream barrier under such conditions. 

If northern pike were to ascend the channel further, they would next encounter a short 

segment of shallow, braided channels (which at higher flows would likely be passable) before 

encountering a largely intact, j-shaped abandoned beaver dam approximately 200 ft in length 

(Photos A-3 and –A-4, Figure A-1). 

Although the northern end of the beaver dam was breached, under the observed 

conditions water was exiting the beaver flowage via leakage rather than through the breach 

directly to a channel. During the second site visit, water depth had increased by approximately 

one foot, but water still was exiting via leakage. 

Under these conditions the beaver dam creates an impassable upstream passage barrier. 

Transect W-2 depicts crest and toe elevations along the axis of the dam, and also the elevation of 

spring high water elevation of the channel immediately below the beaver dam (Figure A-3). 

Under spring conditions it does appear that the channel below the dam can backwater to an 

elevation greater than the breach invert, which could briefly facilitate upstream fish movement, 

particularly if the beaver pond water elevation was high, which is probable during spring run-off. 

Given the ephemeral nature of beaver dams, it is also possible that the shape, size of the dam and 

invert elevation of breaches can change from year to year, so that the observed passage 

conditions can potentially change from year to year. 

A-2

Figure A-1: Orientation of Study Site at the Trough Connection between Wangan Brook and Sanborn Brook Drainages. Transect W-1 

bisects the connector at a constriction with large cobble and boulders; transect W-2 is a longitudinal profile of an abandoned 

beaver dam (not drawn to scale). 

A-3

Figure A-2: Transect W-1. Water and Channel Elevations Wangan Brook and Connector Trough from Sanborn Brook. Cross-sectional 

view looking upstream. 

A-4

Photo A-3: View from within Sanborn Brook beaver flowage looking toward the connector 

channel outlet at crest of dam, panned to the north, breach is at far right. 

Photo A-4: View from within beaver flowage looking toward the connector channel outlet 

downstream at crest of dam, panned to the south. 

A-5

Figure A-3: Transect W-2. Crest, toe and high water elevations at beaver dam dividing the Sanborn Brook and Wangan Brook watersheds. 

Cross-sectional view looking upstream. 

A-6

Response to Comments and Suggested changes to the 

Draft Operational Plan for the Restoration of Diadromous Fishes to the Penobscot 

River 

7-2-09 

Section 1 

Comment: While hatcheries are an important short-term aspect of fishery restoration, in 

the long run hatcheries are not the answer. An active effort is needed to restore the 

fisheries, and short-term measureable results are needed to overcome the political 

issues. 

Response: DMR’s goal of restoring American shad to their historic abundance within a 

50-year period is only possible with a stocking program. Adult returns in excess of 

broodstock needed for the hatchery (1200 fish annually) will be allowed to migrate 

upriver and spawn naturally. Safe and efficient shad passage at Milford, Howland, West 

Enfield, and Mattaceunk (Weldon) is essential for natural expansion of this portion of the 

population. 

In order to meet the objectives of our long-term strategic plan for Atlantic salmon, 

the role of hatcheries needs to be reduced or eliminated. However, given the timeframe 

of the operational plan, we don’t foresee a reduction in our reliance on hatcheries. We 

are trying to maximize the benefit of hatchery products, reduce sea-run broodstock 

requirement in an effort to increase natural spawning. 

The plan states under the Atlantic salmon introduction (p28) ”Pending 

improvement in marine survival rates and freshwater production, hatchery 

supplementation will continue to play a vital role in an integrated management 

approach.” Hatcheries are an interim tool to maintain and possibly increase salmon 

abundances. The term “interim” is used rather than “short-term”, because we have no 

idea when and if marine survival will improve. It is accepted that low marine survival is 

a major factor in the decline of Atlantic salmon in Maine. In order to increase 

escapement we need to have more adult salmon returning or find ways to reduce 

broodstock requirements. Strategies 12.2 and 12.3 (p31) relate to reducing sea-run 

broodstock and thus increase escapement. The other strategies under objective 12 

(p30) are an effort to increase natural spawning. Objective 13, strategies 13.1 and 13.2 

(p31) recognize that by increasing the survival of hatchery products (either in the 

hatchery of in the wild) broodstock requirements are reduced or adult returns increase. 

Strategy 15.1 (p31) recognizes that increasing hatchery production to gain more returns 

can offset low freshwater and marine survival. It must also be recognized that at some 

point densities could become an issue; however, in is unlikely that our hatcheries could 

produce enough salmon for that to become an issue. Thus, this operational plan 

emphasizes using hatcheries and hatchery products as a means to increase adult 

returns, spawning escapement and ultimately natural reproduction. At the same time 

that we are trying to increase upstream escapement of adults salmon they must also be 

able to reach quality spawning habitat. For example, if we increase spawning 

escapement by 100 salmon, but they need to ascend 5 fishways that are 90% efficient, 

the effective escapement is only 60 salmon. In some instance passage at some 

facilities could be as low as 20% or even zero at times depending on flow conditions 

PRFP Page 330

and maintenance operations at a facility. No one strategy will be effective in increasing 

salmon abundances, but collectively they will have a positive impact. 

Comment: Include a provision for a Stocking Management Plan for all stocking efforts to 

address elements such as: identification of broodstock source, numbers of broodstock 

used, disposition of broodstock, calculation of effective population size, life stage 

stocked, date/time of stocking, location of stocking and numbers stocked. 

Response: Information pertaining to many of these elements is included in the alewife 

and shad sections of the Operational Plan (P11, P14, P21, P25), and will be included in 

the Penobscot annual report. There are also three tasks that relate to stocking and 

broodstock management for Atlantic salmon. Task 12.1.1 (p37) calls for the 

development of a Broodstock Management Plan, which will outline a strategy for the 

disposition of adult returns, use or collections of alternate life stages as broodstock, 

target numbers; including best use of the captive reared line, effective population size 

and minimizing domestication effects. Task 12.1.2 (p38) is a related task that 

specifically addresses the use of hatchery versus wild returns. Broodstock 

requirements are based on how many and what products are needed for stocking and 

hatchery capacities. Task 13.2.1 (p41) is the development of an integrated stocking 

adaptive management plan. This plan will develop an integrated stocking strategy that 

will maximize the benefit of each life stage being stocked with the goal of increase 

returns of adult salmon that are motivated to migrate towards quality spawning habitat. 

Both tasks are closely related and will need to be developed concurrently. 

Alewives 

Comment: Disappointment was expressed that the State is not stocking alewives in 

Fields Pond this year and would like to see fish stocked there as soon as possible. 

Response: NOAA and UM requested that DMR not stock Fields Pond, because there is 

an ongoing study to assess natural (unstocked) recolonization following removal of two 

downstream dams. 

Comment: Concern about what alewives would do to the fish present in ponds. 

Response: DEP, DIFW, and DMR conducted a 10-year study between 1987 and 1996 

to examine the impacts of stocking alewives on existing fish populations in Lake 

George. The study encompassed a four-year period “before” alewife stocking, a threeyear 

period “during” alewife stocking, and a three-year period “after” alewife stocking. 

None of the major (brown trout, smallmouth bass, chain pickerel, and white perch) or 

minor sportfish (brown bullhead, burbot, pumpkinseed sunfish, redbreast sunfish, and 

yellow perch) showed a difference in average length or weight when “before” and “after” 

periods were compared. The impact of alewife stocking on smelt abundance was 

confounded by a commercial smelt fishery that occurred during study, and sampling 

methods that removed a large number of pre-spawn smelt in the “before” period. 

However, young-of-year smelt grew significantly faster “during” alewife stocking. 

Comment: Concerns over early mortality syndrome in salmonids due to thiamine in east 

coast alewives. 

PRFP Page 331

Response: Early mortality syndrome (EMS) is a non-infectious disease, associated with 

low thiamine that affects lake trout and other salmonids. Most reports of EMS are from 

the Great Lakes and New York Finger Lakes, where native forage fish (e.g. emerald 

shiner) have declined and have been replaced by non-native land-locked alewife that 

can contain high levels of thiaminase, an enzyme that breaks down thiamine. 

Most of the studies from the Great Lakes stress that land-locked alewife are the 

primary forage species of the salmonids that have exhibited EMS (Honeyfield et al. 

2005). In recent years a decline in the landlocked alewife abundance has resulted in a 

recovery of the wild lake trout population in some of the Great Lakes. An increased 

percentage of other forage species in the diet seems to offset the effects of thiaminase 

in the alewives. 

Anadromous alewives are in lakes for only a portion of the year, May to October. 

In Echo Lake, Maine, where landlocked alewives were introduced, alewives were 

seasonal food for landlocked Atlantic salmon, while smelt were eaten all year (Lackey 

1969, Speirs 1974). Thus, smelt not alewives were the primary forage species for 

landlocked Atlantic salmon. This seasonality in the diets of landlocked salmon is, in part, 

because the two prey species inhabit different parts of lakes. In the summer months 

juvenile alewives are found above the thermocline in the littoral and pelagic zones of 

lakes (Lackey 1970). In these months, juvenile and adult smelt migrate diurnally from 

deeper water into the thermocline to feed, making them more available to salmon and 

lake trout that feed in or below the thermocline. 

Most landlocked salmon fisheries in PN watershed lakes are supported by stocking, 

not natural reproduction. During the period of sea-run alewife introductions into Lake 

George no significant changes in the average size and weight of stocked brown trout 

were observed. 

Honeyfield, D. C., J. P. Hinterkopf, J. D. Fitzsimons, D. E. Tillitt, J. L. Zajicek and S. B. 

Brown. 2005. Development of Thiamine Deficiencies and Early Mortality 

Syndrome in Lake Trout by Feeding Experimental and Feral Fish Diets 

Containing Thiaminase. Journal of Aquatic Animal Health 17: 4-12. 

Lackey, R.T. 1969. Food Interrelationships of Salmon, Trout, Alewives, and Smelt in a 

Maine Lake. Transactions of the American Fisheries Society. 98(4): 641–646. 

Lackey, R.T. 1970. Seasonal depth distribution of landlocked Salmon, Brook Trout, 

landlocked Alewives, and American Smelt in a small Lake. Journal Fisheries 

Research Board of Canada. 27(9): 1656–1660. 

Spiers, G.D. 1974. Food Habits of Landlocked Salmon and Brook Trout in a Maine Lake 

after Introduction of Landlocked Alewives. Transactions of the American 

Fisheries Society. 103(2): 396–399. 

Comment: How we will determine success at Howland and other lakes? 

Response: Success will be determined primarily by annual counts of returning adult 

alewife at Milford, West Enfield, Pumpkin Hill and Howland (6.1.4 on P10, P23), and 

secondarily by biweekly beach seine surveys for juvenile fish (6.1.6 on P10, P23). 

Counts at Howland may require special techniques (e.g. videotaping); if this is not 

feasible, alewife returns to may have to be monitored at the appropriate lake outlet. 

PRFP Page 332

Comment: Several people requested that we better define the timetable for Schoodic, 

Seboeis, and Sebec and note Phase 2 and 3 timetables to clarify plans in the future. 

Response: DMR will use a three-phased approach for alewife restoration with each 

phase potentially requiring up to 16 years of annual stocking. Within these broad 

categories, lakes will be prioritized based on previously described attributes. Lakes 

identified as Phase 1 in the Operational Plan remain unchanged. Phase 2 and Phase 3 

lakes will be stocked using broodstock collected at the Milford fishlift. Phase 3 lakes, 

which were cooperatively identified by DMR and DIFW, will be stocked last, and some 

will require further investigation before stocking. Phase 3 waters include Cold Stream 

Pond, Upper Cold Stream Pond, Nicatous Lake, West Lake, Duck Lake, Gassabias 

Lake, Seboeis Lake, Schoodic Lake, Sebec Lake, Piper Pond, Upper Pond, and 

Pleasant Lake). Collectively these lakes are the source water for a hatchery, support 

classic cold-water fisheries, are blocked to prevent spread of pike, or may be above 

historically impassable falls. The remaining lakes are included in Phase 2. 

Comment: A commenter recommends a reduction in the extent of Phase I alewife 

restoration from 13 to 7 historical lakes (Chemo, Pushaw, Boyd, Little Pushaw, Mud, 

Saponac, and Madagascal), lakes to which there is presently access without the need 

for passage through either the Howland or West Enfield dams. 

Response: Phase I alewife lakes were purposely chosen to include historical habitat 

above the Howland, West Enfield, and Pumpkin Hill dams. Passage efficiency at these 

dams needs to be assessed for multiple species, and improved if necessary. The most 

cost-effective approach is to test efficiency for all species in a limited time frame, and 

make improvements once that benefit all species. In addition, the Settlement 

Agreement provides for a 15-year period after the Milford fishlift becomes operational 

for effectiveness testing of the Howland bypass. 

Comment: NOAA and USFWS comments on alewife restoration concern the source of 

broodstock to be used. USFWS recommends that the Plan states that: 1) a priority is 

placed on using in-basin broodstock sources for alewives to the greatest extent 

possible; 2) if it is determined that out-of-basin broodstock sources are necessary, 

follow the “next nearest neighbor concept” in selecting sources of fish to stock the 

Penobscot, and 3) that waterbodies that are initially stocked with in-basin fish should be 

limited to the use of those same in-basin sources. In a case where the in-basin source 

is not large enough to fully meet the stocking requirement, then in-basin sources should 

be used first; other sources could then be used to meet the remaining fish requirement. 

NOAA recommends inclusion of the decision process for assessing feasibility of 

different broodstock sources. 

Response: DMR’s experience is that successful alewife restoration does not require inbasin 

or next-nearest-neighbor sources of broodstock. For example, the large alewife 

population (>1.3 million in 2009) on the Sebasticook River was restored using 

Androscoggin River broodstock, which was restored using Royal River broodstock, 

which was stocked with fish from the Damariscotta River. However, we have stated our 

willingness to use in-basin broodstock as a first option and next-nearest-neighbor 

broodstock as a second option if certain conditions are met. The conditions are: 1) on 

the basis of existing information DMR, NOAA, and USFWS determine that a donor 

PRFP Page 333

population can provide 97,500 alewife annually for up to 16 years without harm to the 

donor population; 2) new funding is available for constructing or upgrading a trappingsorting 

facility for safely obtaining the broodstock, and this facility must be operational 

by May 1, 2011 at the latest; 3) new funding is available for trucks and staff to carry out 

stocking beginning May 1, 2011 at the latest; and 5) if broodstock are obtained from a 

town with fishing rights the town must be reimbursed for lost revenue. As we have 

previously stated, if stocking must be done with existing staff and equipment dedicated 

to the Kennebec and Androscoggin restoration projects, fiscal and programmatic 

constraints dictate the use of broodstock from those two rivers. 

Comment: If exogenous fish stocks are used during Phase 1, what would the target 

count at the Milford Project fishway for deciding when Phase 1 stocking would switch 

from an exogenous source to an in-basin source? 

Response: Target for switch is ~532,000. 

Comment: A cost should be estimated for developing in-basin trapping facilities at 

Souadabscook Stream and the Orland River for alewife as part of work item number 

7.1.2. 

Response: Work item (s/b) 6.1.2 is to develop cost estimates, which will require 

engineer to review sites. 

Shad 

Comment: A commenter recommends reducing the extent of Group I river reaches for 

shad restoration to “Milford Dam to West Enfield dam”, and “Passadumkeag mouth to 

Lowell Dam”. 

Response: Phase I shad habitat was purposely chosen to include historical habitat 

above the Howland, West Enfield, and Pumpkin Hill dams. Passage efficiency at these 

dams needs to be assessed for multiple species, and improved if necessary. The most 

cost-effective approach is to test efficiency for all species in a limited time frame, and 

make improvements once that benefit all species. In addition, the Settlement 

Agreement provides for a 15-year period after the Milford fishlift becomes operational 

for effectiveness testing of the Howland bypass. 

Comment: Collectively, NOAA and USFWS recommendations regarding shad 

restoration include 1) delaying action until the number of shad returning to Milford has 

been evaluated for 2-3 years, 2) developing an adaptive management plan or decision 

tree that would determine management alternatives (natural recolonization vs. hatchery 

supplementation using in-basin broodstock vs. hatchery supplementation using out-ofbasin 

broodstock) based on thresholds of fish captured in the Milford fishway, and 3) 

developing a Stocking Management Plan or a Broodstock Management Plan. 

Response: Neither NOAA nor USFWS has criticized DMR’s objective of restoring shad 

to historical habitat and abundance in 40-50 years nor have they criticized our estimates 

of abundance, so DMR will continue to use these targets. DMR developed two models 

to explore scenarios that were likely to achieve restoration in the 40-50 year time frame 

(8-10 shad generations). These models are simple, because there is a paucity of 

demographic data for shad. The first model explores the possibility of achieving the 

PRFP Page 334

estoration objective by natural recolonization; it uses a range of starting population 

sizes and intrinsic rates of increase from one generation to the next (Table 1). The 

model indicates that achieving Measure 7.1 (633,300 adult shad returns in 35-40 years) 

by natural recolonization would require either a very high rate of increase for a 

prolonged period or a very large starting population. For example, this target could be 

reached with a starting population of 2500-5000 fish that on average doubled in 

abundance every five years. This level of reproduction might be expected in bacteria, 

but not in shad. If the rate of reproduction is reduced to 1.5 or 1.25, the size of the 

starting population would have to be 40,000 to 135,000 fish. DMR is not aware of shad 

populations in Maine or elsewhere that consistently are achieving these levels of 

reproduction; remnant populations on the east coast that have been greater than about 

1000 fish; or any large river restoration that has been accomplished by natural 

recolonization. DMR has concluded that reliance on natural recolonization is not a valid 

management strategy. 

DMR next modeled restoration at two fry stocking levels (Table 2). The model 

assumes one adult return for each 318 hatchery fry released and 100 adult returns for 

each 86 spawning adults (reproduction rate = 1.1627907) based on data presented in 

Restoration of American Shad to the Susquehanna River: Annual Progress Report 

2000. For simplicity the model assumes a starting population of 0 and no repeat 

spawning. While reformatting the model for presentation, DMR discovered an error in 

its original calculations. The corrected model indicates that fry stocking would have to 

continue for a longer period of time than originally reported, and that the higher stocking 

rates are needed to achieve the shad restoration objective. 

DMR considered the consequences of the recommendation made by USFWS and 

NOAA to delay an active restoration program. Delaying activity for at least five years 

would make it more difficult to reach the achievable population target of 633,000 fish in 

50 years. There is no guarantee that the private Waldoboro Hatchery would be 

available to produce shad after a five-year hiatus, and there currently are no other 

hatcheries in New England with the capacity or capability of producing 12 million shad 

fry. In addition, the proposed schedule for testing passage effectiveness at mainstem 

dams for multiple species and making improvements at a single time would be 

jeopardized. DMR has determined that delaying active restoration carries too great a 

risk for the restoration. 

The State and federal agencies have not come to agreement about the source of 

broodstock that would be used to produce hatchery-reared fry. Potential sources of 

1200 adult shad remain as limited as they were when the Strategic Plan to Restore 

American Shad (Alosa sapidissima) to the Penobscot River, Maine was completed in 

2001. NOAA has recommended an extensive comparison of biological characteristics 

(e.g. degree of iteroparity, age at maturity, duration of freshwater rearing, migration 

distance to spawning ground) of stocks within 500 miles of the Penobscot. We believe 

this recommendation is unrealistic. DMR’s experience is that minimum mortality occurs 

if total transport time of adult shad broodstock is 3 hours or less, and that mortality 

significantly increases, especially for large females, when total transport time is 5 hours 

or more. The Operational Plan compares potential broodstock sources in the Gulf of 

Maine with a maximum transport time of 5 hours (Table 3). The Merrimack is the only 

population that can provide sufficient broodstock with certainty. 

PRFP Page 335

DMR proposes to expand the Waldoboro shad hatchery and initiate a fry-stocking 

program on the Penobscot using broodstock from the Merrimack. DMR proposes to 

stock the fry above Howland, so the bypass can be assessed. When sufficient shad 

returns (1200) are captured at Milford they can be used as broodstock. 

Table 1. Results of natural recolonization model. 

Generational expansion rate = 2 Generational expansion rate = 1.5 


1 1,000 2,500 5,000 1 1,000 2,500 5,000 40,000 

6 2,000 5,000 10,000 6 1,500 3,750 7,500 60,000 

11 4,000 10,000 20,000 11 2,250 5,625 11,250 90,000 

16 8,000 20,000 40,000 16 3,375 8,438 16,875 135,000 

21 16,000 40,000 80,000 21 5,063 12,656 25,313 202,500 

26 32,000 80,000 160,000 26 7,594 18,984 37,969 303,750 

31 64,000 160,000 320,000 31 11,391 28,477 56,953 455,625 

36 128,000 320,000 640,000 36 17,086 42,715 85,430 683,438 

41 256,000 640,000 1,280,000 41 25,629 64,072 128,145 1,025,156 

46 512,000 1,280,000 2,560,000 46 38,443 96,108 192,217 1,537,734 

51 1,024,000 2,560,000 51 57,665 144,163 288,325 2,306,602 

56 2,048,000 56 86,498 216,244 432,488 3,459,902 

Generational expansion rate = 1.25 Generational expansion rate = 1.16 


1 1,000 2,500 135,000 1 1,000 2,500 135,000 225,000 

6 1,250 3,125 168,750 6 1,163 2,907 156,977 261,628 

11 1,563 3,906 210,938 11 1,352 3,380 182,531 304,218 

16 1,953 4,883 263,672 16 1,572 3,930 212,245 353,742 

21 2,441 6,104 329,590 21 1,828 4,570 246,797 411,328 

26 3,052 7,629 411,987 26 2,126 5,314 286,973 478,289 

31 3,815 9,537 514,984 31 2,472 6,179 333,690 556,150 

36 4,768 11,921 643,730 36 2,874 7,185 388,012 646,686 

41 5,960 14,901 804,663 41 3,342 8,355 451,176 751,960 

46 7,451 18,626 1,005,828 46 3,886 9,715 524,623 874,372 

51 9,313 23,283 1,257,285 51 4,519 11,297 610,027 1,016,712 

56 11,642 29,104 1,571,607 56 5,254 13,136 709,334 1,182,223 

Measure 7.1: 633,300 adult shad returns in 35-40 years 

PRFP Page 336

Table 2. Results of fry stocking model. 

318 fry to adult 1.162790698 generational reproductive rate 


Return 

Annual 

adult 

years returns Y1-5 Y6-10 Y11-15 Y16-20 Y21-25 Y26-30 Y31-35 Y36-40 Y41-45 Y46-51 

6,000,000 6,000,000 6,000,000 6,000,000 6,000,000 6,000,000 6,000,000 6,000,000 6,000,000 6,000,000 

Y6-10 18,868 18,868 

Y11-15 40,807 21,939 18,868 

Y16-20 66,318 25,511 21,939 18,868 

Y21-25 95,982 29,664 25,511 21,939 18,868 

Y26-30 130,475 34,493 29,664 25,511 21,939 18,868 

Y31-35 170,583 40,108 34,493 29,664 25,511 21,939 18,868 

Y36-40 217,221 46,637 40,108 34,493 29,664 25,511 21,939 18,868 

Y41-45 271,450 54,229 46,637 40,108 34,493 29,664 25,511 21,939 18,868 

Y46-50 334,508 63,057 54,229 46,637 40,108 34,493 29,664 25,511 21,939 18,868 

Y51-55 407,830 73,323 63,057 54,229 46,637 40,108 34,493 29,664 25,511 21,939 18,868 

Y56-60 474,221 85,259 73,323 63,057 54,229 46,637 40,108 34,493 29,664 25,511 21,939 

Y61-65 551,420 99,138 85,259 73,323 63,057 54,229 46,637 40,108 34,493 29,664 25,511 

Y66 641,186 115,277 99,138 85,259 73,323 63,057 54,229 46,637 40,108 34,493 29,664 

Return 

years 


Annual 

adult 

returns Y1-5 Y6-10 Y11-15 Y16-20 Y21-25 Y26-30 Y31-35 Y36-40 Y41-45 Y46-51 

12,000,000 12,000,000 12,000,000 12,000,000 12,000,000 12,000,000 12,000,000 12,000,000 12,000,000 12,000,000 

Y6-10 37,736 37,736 

Y11-15 81,615 43,879 37,736 

Y16-20 132,637 51,022 43,879 37,736 

Y21-25 191,965 59,328 51,022 43,879 37,736 

Y26-30 260,950 68,986 59,328 51,022 43,879 37,736 

Y31-35 341,167 80,216 68,986 59,328 51,022 43,879 37,736 

Y36-40 434,441 93,275 80,216 68,986 59,328 51,022 43,879 37,736 

Y41-45 542,900 108,459 93,275 80,216 68,986 59,328 51,022 43,879 37,736 

Y46-50 669,015 126,115 108,459 93,275 80,216 68,986 59,328 51,022 43,879 37,736 

Table 3. Nearest potential sources of American shad broodstock. 

River system Distance Status of run 

Penobscot 0 mi Size unknown, not easily captured 

Narraguagus 100 adults in 2008 

Kennebec/Androscoggin 58 mi Size unknown, ongoing restoration, not easily 

captured 

Saco 93 mi ~1200 adults, ongoing restoration, capture at 

fishlift 

Merrimack 125 mi ~29,000 in 2008, ongoing restoration, capture at 

fishlift 

St. John 179 mi Less than 1000 in 28 of 29 years from 1974-2002 

Other Diadromous Fish 

Comment: There is a need to stop the commercial fishing for lamprey and perhaps eels. 

Response: DMR is not aware of any commercial harvest for lamprey in the Penobscot 

drainage. Eel harvest in the entire State is a very small percentage of total east coast 

harvest, and would require a legislative change. 

Comment: Has DMR considered other species like sea run white perch? 

Response: We believe all diadromous species are addressed in the plan. Bigelow and 

Schroeder note that white perch are not anadromous in the Gulf of Maine, and they 

have never been caught in our beach seine surveys in the lower river. 

PRFP Page 337

Salmon 

Comment: There are advocates of active Atlantic salmon restoration and would like it to 

be speeded up to 10 years rather than 40. 

Response: Ten years encompasses only two Atlantic salmon generations 

(approximately 5 years per generation). This time frame is far too short for 1) a 

sustained population response, and 2) to implement management actions and adjust as 

the actions are either successful or unsuccessful. Furthermore, longer time frames are 

necessary when habitat improvements are needed for restoration. However, the plan is 

to restore sections of the basin over time: this may result in important sections of the 

basin restored over a much shorter time frame. The 40 year time table is aggressive, 

but allows time to test management strategies and improve management. It also allows 

time for habitat improvements to occur and have an effect on the ecosystem. Finally, 

with limited resources, all possible actions cannot be performed everywhere; therefore a 

phased approach over time is necessary. This timeline is intended to inform managers 

as to how to structure recovery actions over space and time, and to assess progress 

towards recovery objectives. It does not preclude faster recovery, but does provide a 

yardstick by which to measure our progress. 

Comment: A commenter recommended more use of instream hatcheries for salmon. 

Response: The objective of salmon restoration is to establish a self-sustaining salmon 

population. This operational plan was developed to maximize the benefit from 

hatcheries within the constraints of the current salmon program. Ultimately, hatcheries 

would not be needed. With that said, in basin hatcheries would provide many benefits 

to the salmon program. For example, timing of hatching and emergence would be 

synchronized with natural production in the River. However, It is likely that the hatchery 

environment itself is a bigger factor than location. 

Comment: Predation by cormorants and seals is not addressed in the plan. 

Response: Predation of salmon by cormorants and seals is an issue that we are 

concerned about. One hypothesis is that by restoring other diadromous species such 

as alewife, blueback herring, and shad, predators will have an alternative prey base. 

Thus, providing a “prey buffer” for salmon as well as, trout and smallmouth bass. One 

unknown is the possibility of a numerical response, an increase in the abundance of a 

predator species. If food resources are the limiting factor for a predator species, we 

would expect an increase in their population. However, if another factor is limiting their 

abundance, such as roosting sites, then an increase in their forage base would not 

result in a numerical response. 

Comment: Several people expressed skepticism of the fry stocking program. 

Response: Currently, the salmon program is geared towards fry stocking and smolt 

production. There is limited ability to change that in the near-term. However, there are 

several tasks in the operational plan that are directly and indirectly related to fry 

stocking and freshwater production. Task 12.1.1 (p37) the development of a 

Broodstock Management Plan will outline a strategy for the disposition of adult returns. 

The primary objective of the management plan is to increase adult escapement. By 

PRFP Page 338

increasing escapement and increasing natural spawning we hope to reduce the 

emphasis on fry stocking to populate freshwater habitat. An additional series of tasks 

are designed to evaluate all aspects of stocking, from which products are stocked to 

when, where, and how many of each are stocked. Currently, we know that the best 

adult return rates are from stock smolts. However, fry stocking has not been evaluated 

successfully to returning adults. We are not able to distinguish between wild salmon 

and those stocked as fry. Furthermore, no stocking effort has been assessed for 

lifetime fitness, which is the critical measure of a stocking program geared to 

restoration. Stocked smolt may not produce successful adult spawners in the wild. This 

operational plan incorporates an adaptive management approach that will facility 

changes in hatchery production to that increase adult escapement and increase 

freshwater production. In the future, that may or may not include a fry stocking 

program. With that said, this operational plan, with a lifespan of five years, was 

developed to maximizing the benefit from hatchery products within the boundaries of the 

current salmon program. 

Comment: The Service, NOAA-Fisheries and the State of Maine are currently working 

on an Atlantic salmon recovery framework, which is not yet completed. The Plan’s 

operational objectives will need to align with this framework so the Plan will have to 

have some provision to modify the objectives to be consistent with the framework. 

Response: In introductory material we highlight the importance of the framework and in 

Section 5 there are two tasks that clearly indicate the plan will be integrated with 

regional and local management groups. [1: Participate in regional fisheries management 

and assessment efforts at both administrative and scientific levels and 5: Work closely 

with the Atlantic salmon Action Teams.] We could not delay this plan until the 

framework was completed. However, we believe that the operational objectives are 

consistent with objectives discussed during the framework process. The priority of the 

objectives is likely what will be affected as the framework is used to develop portfolios. 

Comment: Since Atlantic Salmon can navigate beyond the exclusion devises at the 

West Enfield and Howland Dams, why would you authorize the removal of exclusion 

devices at both of these dams before passage by other target species is required at 

either dam? 

Response: There is currently no plan to remove the hydraulic barrier at the Howland 

and West Enfield Projects until it is necessary for restoration. For example, the state 

would not consider removing the West Enfield barrier until adult shad or river herring 

return to the site. However, the U.S. Fish and Wildlife Service and NOAA-Fisheries 

may require an assessment of the barrier for Atlantic salmon under the Endangered 

Species Act. Based on this assessment, the Services may request changes to the 

barrier if it delays or impedes the upstream migration of salmon. 

Section 2 - Connectivity 

Comment: It was suggested that an MOU between IFW and DMR to agree upon 

species dispositions at dams be completed before the plan is finalized. 

Response: DMR and IFW will develop and sign a MOU to identify the disposition of nonnative 

species that will be revisited annually. 

PRFP Page 339

Table 4. Species disposition 

Species put back 

Species passed 

Species to be removed 

downriver 

upriver 

Northern pike None identified at this time Native inland species 

Largemouth bass Atlantic salmon 

Central mud minnow alewife 

Black Crappie blueback herring 

Green Sunfish American shad 

Brown trout striped bass 

Rainbow trout sea lamprey 

Splake 

Other non-native / exotic new 

American eel 

species 

Chain pickerel 

Smallmouth bass 

Comment: Objective 16.0 identifies a 90 percent efficiency or higher at fish passage 

facilities for mainstem dams within 10 years to ensure diadromous fish conservation. 

The Service prefers not to prescribe passage efficiencies at fishways and are not able 

to support a performance stand of 90 percent. 

Response: DMR fully understands the Service’s rationale, as it is extremely difficult to 

pinpoint efficiency of passage facilities. There are whole suites of factors that can affect 

passage including discharge, water temperature, timing of arrival at the facility, location 

of the facility, the number of facilities, etc. The comment seems peculiar at this time 

since the Service was a signatory to two recent settlement agreements (Madison Paper 

and Saco) where 80% (interim facilities) and 90% (permanent facilities) passage 

efficiencies were included as performance standards and, to my knowledge, the Service 

did not object to their inclusion. Part of the difficulty with passage is the ambiguity in 

“safe, timely, and effective”. There is no ‘black and white’ in the sense that a facility 

needs to perform at a standard and if it does not, alternatives need to be pursued. For 

example, a passage facility is “safe” if target species pass without injury or death no 

matter how long they take to pass; is “effective” if target species pass the facility 

whether they pass immediately upon approach to the facility or three months after 

approach since the desired result (passage) was achieved; the key is “timely” but even 

the language above – “without detrimental delay” – is vague. When does delay become 

detrimental? We will revise the narrative and objectives accordingly and discuss the 

substitution of “safe, timely, and effective” for efficiency standards. 

Section 3 – Habitat 

Comment: A commenter urged us to include changes to regulations that allow pollution 

and sprawl to occur. 

Response: DEP, DOT, and SPO are the State agencies that have the statutory authority 

to address these issues. We are recommending that we continue to work with these 

agencies in Objective 29. 

Comment: Use references suggested by SHARE in the Habitat Section. 

Response: We will incorporate the SHARE references into the document. 

PRFP Page 340

Section 4 - Non-Native/Northern Pike 

Comment: Several people suggested that the closest fish to compare Northern pike to 

is chain pickerel rather than muskies, which are a riverine fish. 

Response: Chain pickerel and northern pike have many life history similarities, however 

one must be careful about using pickerel as a surrogate for northern pike. The chain 

pickerel has a higher optimal temperature (prefer warmer water) than the northern pike, 

which is clearly indicated by their more southern distributional range. A water body with 

pickerel may not support northern pike at the same densities or even at all if it is too 

warm. Adult northern pike are also known to be more flexible with foraging habitat, 

since they are larger, have a larger relative gape size compared to chain pickerel and 

can be found in deeper, less vegetated areas. 

Comment: The non-native species focused too much on pike, but the other species 

(such as large mouth bass) should be addressed more and would like to see them all 

removed. 

Response: The State of Maine has developed an advisory list of over 80 invasive 

species that includes northern pike, however the state has not gone as far as to include 

pike in a regulatory definition of an invasive species as it has done with certain aquatic 

invasive plants. The state’s advisory list recommends selective control and 

management for northern pike. This approach of selective control and management 

has also been used for other species, such as smallmouth bass. For example, the 

Maine Department of Inland Fisheries and Wildlife manages smallmouth bass as a 

fishery in many Maine lakes and ponds, however it also works to limit their introduction 

through regulation, law enforcement and angler education. The Departments of Inland 

Fisheries and Wildlife and Marine Resources are working on a MOU to identify species 

that will be removed at Milford (see page 11). MDIFW maintains a list of waterbodies 

with non-native species (table 5 and 6). 

Table 5. Streams with non-native species 

Stream Name LMB PKL SMB CMM BNT 

Alamoosook Lake X 

Alder Stream X 

Babcock Brook X 

Baskahegan Lake X 

Baskahegan Stream X 

Bear Brook X 

Bear Brook-Little Pushaw Pond X 

Black Stream X 

Blackman Stream-Chemo Pond X X X 

Crooked Brook X 

Crossuntic Stream X 

East Branch Seboeis Stream X 

Ebhorse Stream X 

Finn Brook X 

Fish Stream X 

Hoyt Brook X 

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Kingsbury Pond X 

Long Pond X 

Long Pond X 

Lower Black Stream X 

Lower Kenduskeag Stream X 

Lower Marsh Stream X 

Lower Mattamiscontis Stream X 

Lower Mattawamkeag River X 

Lower Seboeis River X 

Lower Souadabscook Stream X 

Macwahoc Brook X 

Mattakeunk Stream X 

Middle Kenduskeag Stream X 

Middle Mattawamkeag River X 

Middle Passadumkeag River-Saponac Pond X 

Molunkus Lake X 

Mud Brook X 

Nicatous Lake X X X 

North Branch Marsh Stream X 

Penobscot River at Orson Island X 

Piscataquis River at Schoodic Stream X 

Sandy Stream X 

Scutaze Stream X 

Sebec Lake X X 

Sebec River X 

Seboeis Stream X 

Sedgeunkedunk Stream X 

Ship Pond Stream X 

Sly Brook-Caribou Lake X 

Upper Marsh Stream X 

Upper Mattawamkeag River X 

Upper Molunkus Stream X 

Upper Pushaw Stream X X X 

West Branch Dead Stream X 

Wytopitlock Stream X 

LMB-large mouth bass 

PKL – pickerel 

SMB – small mouth bass 

CMM – central mud minnow 

BNT – brown trout 

Table 6. Lakes with non-native species 

Lake Name BLC BNT GSF LMB PIK PKL SMB 

Abbee Pond X 

Alamoosook Lake X X X X 

Ambajejus Lake X 

Badger Pond X 

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Basin Pond X 

Baskahegan Lake X X 

Bear Pond X 

Ben Annis Pond X X 

Bennett Pond X 

Big Bennett Pond X X 

Big Madagascal Pond X X 

Bowlin Pond X 

Boyd Lake X X 

Branns Mill Pond (North) X X X 

Branns Mill Pond (South) X X X 

Brewer Lake X 

Cambolasse Pond X X X 

Caribou, Egg & Long Pd X X X 

Cedar Lake X 

Center Pond X 

Chemo Pond X X X 

Cold Stream Pond X X 

Cranberry Pond X 

Crooked Brook Flowage X X 

Crooked Pond X X X 

Crystal Lake X 

Dolby Pond X 

Drake Lake X X 

Dunham Pond X 

East Branch Lake X X 

Ebeemee Lake X X 

Ebeemee Lake (East Pd) X X 

Eddington Pond X X 

Eighteen Pond X 

Elbow Lake X 

Endless Lake X X 

Eskutassis Pond X X 

Etna Pond X X X 

Faulkner Lake X 

Fields Pond X X 

First Buttermilk Pond X 

First Davis Pond X 

Fitts Pond X 

Flinn Pond X 

Folsom Pond X X X 

Garland Pond X X 

Gassabias Lake X 

George Pond X X X 

Grand Lake Sebois X X 

Green Pond X 

Greenleaf Pond X 

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Halfmoon Pond X 

Hammond Pond X X X 

Hancock Pond X X X 

Harlow Pond X X X 

Harriman Pond X 

Haywire Pond X 

Heart Pond X 

Hermon Pond X X X X 

Holbrook Pond X X 

Horseshoe Lake X 

Hot Pond X 

Hothole Pond X X 

Jackson Brook Lake X X 

Jacob Buck Pond X 

Jaquith Pond X 

Jones Pond X 

Kingsbury Pond X 

Little Bennett Pond X X 

Little Madagascal Pond X X 

Little Mattamiscontis Lake X 

Little Pickerel Pond X X 

LIttle Pushaw Pond X X 

Little Salmon Strm Lk X X 

Long Lake X X 

Long Pond X X 

Lower Hot Brook Lake X X 

Lower Jo-Mary Lake X 

Lower Shin Pond X 

Lower Togue Pond X 

Manhancock Pond X X X 

Marr Pond X X 

Mattamiscontis Lake X 

Mattanawcook Pond X X X 

Mattaseunk Lake X X 

Mattawamkeag Lake X X 

Mayfield Pond X 

Middle Jo-Mary Lake X X 

Millinocket Lake X 

Molunkus Lake X X X 

Mud Pond X X X 

Nicatous Lake X X X X 

Nollesemic Lake X 

North Twin Lake X 

Norton Pond X 

Parks Pond X X 

Passamagamet Lake X 

Patten Pond X 

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Pemadumcook Chain Lake X 

Pickerel Pond X 

Piper Pond X 

Pleasant Lake X X 

Pleasant Pond X X 

Plunkett Pond X X 

Pond Farm Pond X 

Private Pond X 

Pug Pond X 

Pushaw Lake X X X X 

Reed Pond X 

Round Pond X X 

Rush Pond X 

Salmon Stream Lake X X 

Salmon Stream Pond X 

Saponac Pond X X 

Schoodic Lake X X 

Sebec Lake X X 

Seboeis Lake X X 

Second Davis Pond X 

Silver Lake X X X X 

Skitacook Lake X 

Snag Pond X X X 

Snow's Pond X 

Snowshoe Lake X X 

South Branch Lake X X 

South Twin Lake X 

Spaulding Lake X X 

Spectacle Ponds (east) X X 

Spectacle Ponds (west) X X 

Spring Lake X 

Swetts Pond X X 

The Basin X X 

Thistle Pond X 

Toddy Pond X X X X 

Tracy Pond X X X 

Turkey Tail Lake X X 

Upper Cold Stream Pond X X 

Upper Ebeemee Lake X X 

Upper Hot Brook Lake X X 

Upper Jo-Mary Lake X X 

Upper Macwahoc Lake X 

Upper Mattawamkeag Lk X X 

Upper Shin Pond X 

Upper Togue Pond X 

Wadleigh Pond X 

Weir Pond X 

PRFP Page 345

West Garland Pond X 

West Lake X X X 

West Lake Basin X X 

White Horse Lake X X 

Williams Pond X 

Wytopitlock Lake X X 

BLC – black crappie 

BNT – brown trout 

GSF – green sunfish 

LMB - large mouth bass 

PIK – northern pike 

PKL – pickerel 

SMB – small mouth bass 

Comment: There were several comments about human introductions of non-native 

species, including suggestions to make the penalties more intense; make enforcement 

a priority and to make catch and kill of all non-native species in the Penobscot 

mandatory. 

Response: MDMR and IFW will work with the Warden Service and the Attorney 

General’s office about changing enforcement. 

Comment: Human introductions are a big problem and we need to solve that problem 

regardless of what happens at Howland. 

Response: The State of Maine is very concerned with the control and appropriate 

management of introduced aquatic species and produced an action plan in 2002 for 

managing introductions. The northern pike risk assessment indicated that humancaused 

introductions are a significant factor in the establishment and dispersal of pike. 

When possible, the State will explore novel approaches to managing introduced species 

and some of these could include increased public education, rewards for information on 

illegal stocking and strict regulations to remove pike that are caught by anglers. 

Comment: It was recommended that the barrier at Howland remain for 10 years and 

that current northern pike suppression efforts continue and be funded for 10 years. 

Response: The Howland by-pass, one aspect of the Penobscot River Restoration 

Project, will allow diadromous species access to the Piscataquis drainage but also 

opens the drainage to natural dispersal of northern pike. Options under the Multiparty 

Settlement Agreement, which the State of Maine is a signatory to, (MPA) were a bypass 

channel without trap and sort facilities, or removal of the dam. Construction of the 

bypass channel rather than dam removal was the preferred alternative by the 

restoration parties as engineering design and hydraulic modeling showed a bypass 

channel could be constructed and provide free-swim upstream and downstream 

passage at the Howland dam, rather than necessitating dam removal. Thorough 

evaluation and engineering design of trap and sort facilities to prevent further upstream 

movements of pike into the Piscataquis River drainage through the bypass channel 

were conducted concurrently. This evaluation determined trap and sort facilities to be 

unfeasible in meeting restoration goals. The fisheries agencies and other parties 

PRFP Page 346

agreed to undertake a formal risk assessment of potential pike movements through the 

channel and into upstream sub-drainages. The measures that the State has taken or 

are proposing in the Plan to control pike are feasible and prudent measures to minimize 

the risk of harm. The benefits of restoring diadromous fish to the Piscataquis River 

watershed, in light of the management actions currently in place and proposed to 

control the risks of northern pike in the watershed, outweigh any potential negative 

impacts. 

Control measures have been implemented by the State of Maine and its partners 

for the population of northern pike in Pushaw Lake and Mud Pond. IFW will be 

sampling Pushaw Stream in June to try and determine if pike have colonized (and to 

what extent) in the stream. If a large viable population is found, then we may need to 

rethink our efforts at Pushaw Lake. The current information indicates that this population 

has not caused economic harm or harm to human, animal or plant health nor has it 

dispersed widely since its human-caused introduction. The Plan provides additional 

measures to selectively control and manage this introduction. 

Comment: Will there be any restrictions against stocking rainbow trout in farm ponds? 

Response: IFW traditionally asks DMR for comments prior to permitting farm/private 

pond stocking in the Penobscot drainage. A new written MOU is being developed that 

states MIFW will permit the stocking of Rainbow and Brown trout in private ponds within 

in the Penobscot River drainage, provided the pond has no outlet. An exception to this 

rule is if a pond without an outlet is in close proximity to the river or a tributary and there 

is potential for fish to escape during any high water event. All ponds in question are to 

be inspected by MIFW or MDMR staff prior to allocation of a permit from MIFW for 

species other than brook trout. 

Comment: The Northern pike risk assessment under estimates the risk of pike. 

Response: The risk assessment used the best available science and expertise from 

state and federal agencies within Maine. The assessment represents a biological 

opinion on the ecological harm that may be associated with a pike introduction, the 

pathways for introduction, the potential habitat that may be impacted and the current 

quality of that habitat for native species. While there is some uncertainty in the opinion 

due to limited information, it provides specific steps that will limit the distribution of 

natural dispersal of pike in the watershed at known barriers and proposes measures to 

control illegal introductions. 

Comment: Several comments suggested that Executive Order 13112 and Maine State 

law prohibit the introduction of non-native species, which means the State and Federal 

agencies are violating the law as the Northern Pike an illegal introduction and suggest 

amending the plan to maintain consistency with established State and Federal policy. 

The suggested amendments were to keep the Howland and Enfield Dams as barriers to 

upstream movement of pike and other invasive species. 

Response: In their June 8, 2009 comments on the draft Plan, the U.S. Fish and Wildlife 

Service provided their opinion on the Service’s consistency with Executive Order 13112 

on Invasive Species related to the Penobscot River Restoration Project. The Service 

does not believe that any of the actions it has taken are likely to cause or promote the 

PRFP Page 347

spread of any invasive species, and has determined that, even if there were a risk of 

spread, the benefits of the Penobscot River Restoration Project clearly outweigh the 

potential harm. They further explain that the available information on northern pike in 

the Penobscot River watershed does not indicate that it has caused economic harm or 

harm to human, animal or plant health nor has it dispersed widely since its humancaused 

introduction. The Service was involved in assisting to complete the northern 

pike risk assessment and they stated that the additional measures to selectively control 

and manage this introduction are feasible and prudent measures to minimize the risk of 

harm. 

The Service also explained that Section 2(2)(iv) of the Executive Order calls for the 

restoration of native species and habitats to reduce the effects of invasive species and 

to prevent further invasions. Consequently, they believe that this Plan and the elements 

in Lower Penobscot River Multiparty Settlement Agreement are consistent with the 

Executive Order because they are meant to restore diadromous fish to the watershed. 

The State of Maine has developed an advisory list of over 80 invasive species that 

includes northern pike (located in Appendix D of the State of Maine Action Plan For 

Managing Invasive Aquatic Species), however the state has not gone as far as to 

include pike in a regulatory definition of an invasive species as it has done with certain 

aquatic invasive plants (Title 38: Chapter 3: Subchapter 1: §410-N. Aquatic nuisance 

species control). In and of itself, the advisory list is not a regulation or law. The state’s 

advisory list recommends selective control and management for Northern pike, which 

have been implemented by the state and its partners for the population of northern pike 

in Pushaw Lake and Mud Pond. The northern pike risk assessment provides additional 

measures to selectively control and manage this introduction. The Action Plan notes, as 

does the risk assessment, illegal introductions are the main pathway for this species. 

The measures that the state has taken or are proposing to control pike are feasible and 

prudent measures to minimize the risk of harm. 

Comment: What is the projected time frame that the pike could make it up the river if the 

barriers are removed? 

Response: No data or methods were readily available to predict the rate of natural 

dispersal of northern pike. We believe that the natural dispersal rate would be low 

because of several life history traits: 

1. Northern pike have a narrow optimum temperature range of between 19 and 21º 

C. This temperature range is often exceeded in the summer months on the 

mainstem rivers; 

2. Northern pike are generally sedentary and do not move great distances (2 

kilometers). This behavior has been documented in Pushaw Lake through radio 

telemetry; 

3. The greatest movement of pike occurs during the spawning period in early spring 

and there is some indication in the literature that it may be related to a return to 

natal spawning sites as opposed to dispersal to new sites; 

4. Pike dispersal appears to be related to an increase in density. The density of 

pike in Pushaw Lake appears to be low so we do not expect density-dependent 

movement to occur in the near future; 

PRFP Page 348

5. Pike spawning and nursery habitat is typically contiguous and requires emergent 

wetland so dispersing populations would be associated with wetland complexes 

and with those wetland complexes that are closest to an existing population. 

There are sections of the Penobscot River that have little emergent wetland, 

which would likely slow dispersal of pike upstream; and 

6. Pike prefer lentic or non-flowing water so rivers with even moderate flow are a 

less preferred habitat. This habitat preference would favor a low natural 

dispersal rate through mainstem river corridors. 

These aspects of pike biology lead us to conclude that human-caused introductions are 

a greater threat than natural dispersal within the Penobscot River watershed. 

Comment: Stocked brown trout would have a greater impact on native species than 

northern pike. 

Response: Brown trout, an exotic species native to Europe, is currently stocked by 

MDIFW for recreational fishing in Nicatous Lake located above a set of falls impassable 

to all species of fish but Atlantic salmon. IFW and DMR are working on an MOU to be 

revisited every five years to continue this effort. Nicatous Lake is a 5,165 acre lake 

located T40 MD in Hancock County. It is managed for both warm water (chain pickerel, 

smallmouth bass, and white perch) and cold water (brown trout and landlocked salmon) 

species of game fish. 

Brown trout were stocked in Nicatous Lake historically from 1938 to 1942, and 

more recently from 1998 to the present. The lake was managed as a principal fishery 

for stocked landlocked salmon from 1971 to 1997, but due to poor growth and holdover, 

a management decision was made to switch to brown trout, a hardier coldwater species 

of fish and a less discriminate forager than salmon. Currently 4,000 fall yearling age 

brown trout (18 month old) and 1,500 spring yearling age landlocked salmon (12 month 

old) are stocked annually. The next sport fish survey (winter creel census) is scheduled 

for winter 2010 or 2011. 

MIFW will continue to stock brown trout at Nicatous Lake for the next 5 years 

(2014). During this time period at least one winter sport fish survey will be conducted 

and volunteer angler book data will be synthesized to determine the importance of the 

Nicatous Lake brown trout fishery to the angling public. In addition, regional staff will 

conduct one or more summer lake habitat (basic water quality) and fish sample surveys 

(gill netting or trap netting) to determine if management goals (age and growth) are 

being met. At the end of the five year period a final report will be developed and the 

interagency MOU for the brown trout stocking program at Nicatous Lake revisited. 

Comment: The tasks designed to assess the risks associated with non-native species 

should include an additional provision to obtain more information about the ecological 

effects of pike where they occur in other Maine waters, especially in lotic habitats. 

Response: We agree that the risks associated with introduced species need further 

research in Maine and have revised the plan to include this topic in the adaptive 

management planning effort. 

Comment: How will the migration of alewives affect pike? 

PRFP Page 349

Response: There are conditions when pike may have a less sedentary and more 

pelagic feeding behavior, however these conditions are typically related to a lack of prey 

to sustain them in their preferred habitat. Another period that female pike may feed 

more pelagicly is in the fall during egg development. During this period, female pike 

must increase body weight by 10 to 30 percent, which may require them to forage in a 

larger than normal home range to meet this physiological need. 

No observations have been documented on the interaction of anadromous 

alewife and pike. In the Great Lakes, the landlocked alewife is a preferred prey for adult 

pike and they have been observed feeding on alewife from areas of cover. During 

conditions of low food availability, adult pike may exploit adult alewife in lentic habitats 

however juvenile alewife are likely to be too small to be preferred prey for most size 

classes of pike. 

Comment: What criteria were used in northern pike habitat model? 

Response: The potential habitat model was developed through information reported in 

the literature, available data on the lakes, and verified by applying it to ponds and lakes 

in the Belgrade area where northern pike have existed and been managed for many 

years. The model predictions were compared to the predictions of the local biologists 

that were developed based on professional judgment. The model was not perfect (17% 

of the lakes were classified by the model as being lower in potential than identified by 

the local biologist) so it is likely that not all the lakes were classified properly. 

The model used a three-tiered scale: low, medium or high habitat potential. The 

rank was assigned for lakes and ponds by assessing nine habitat parameters based on 

the published literature. The rank reflects the relative habitat conditions for pike based 

on the nine parameters, what is know about the species-habitat relationships and 

assumes a positive relationship between habitat condition and population capacity (the 

pike population will be related to the suitability of the habitat). 

The model is useful because it provides an a priori method to rank lakes (a 

process that is repeatable and applied without bias), it provides a method to rank lakes 

when there is limited knowledge (there are hundreds of lakes in the Piscataquis River 

watershed and most have not been extensively surveyed), it provides a predictive 

capability, it is practical to implement, and it allows a structured decision making 

process that is based on the literature. One step that was not completed prior to the 

release of the draft plan is to review the list with the local biologists and adjust it based 

on professional judgment. We intend to do this next step for the final plan. 

Comment: Several people requested that the MOUs on Schoodic, Seboeis, and Sebec 

be clarified. 

Response: DMR and IFW will develop and sign a MOU to keep barriers in place on 

Sebec, Dover (whichever provides the best option), Seboeis, and Schoodic to be 

revisited at a minimum of every 5 years. We will consult with the Services at the time of 

renewal. 

a. Sebec Lake (Phase 3 alewife lake): Maintain current blockages for invasive fish 

species at the outlet of Sebec Lake and on the Sebec River at the Milo Hydro 

Project until such time that Phase 2 alewife restoration is complete. 

PRFP Page 350

. Schoodic Lake (Phase 3 alewife lake): Maintain current blockages for invasive 

fish species at the outlet of Schoodic Lake until such time that Phase 2 alewife 

restoration is complete. 

c. Seboeis Lake (Phase 3 alewife lake): Maintain current blockages for invasive 

fish species at the outlet of Seboeis Lake until such time that Phase 2 alewife 


d. Piscataquis River (Dover-Foxcroft and Guilford): Create and maintain a minimum 

30-inch vertical jump barrier to preclude upstream passage of invasive fish 

species while still allowing Atlantic salmon to pass upstream at one or more of 

the upstream passage facilities located at Brown’s Mill, Moosehead 

Manufacturing, and Guilford. Keep the barrier in place at least until such time 

that Phase 1 alewife restoration is complete and Group 1 American shad 


Section 5 – Communication etc 

Comment: The science is sound but a greater emphasis on the outreach is needed. 

Education of the general public as to the benefits and importance of alewife restoration 

is absolutely vital and there should be a stronger focus in the plan. 

Response: We propose to add a task to Objective 27 that reads: Develop an outreach 

strategy that incorporates the tasks that follow and identifies additional ways to educate 

the general public on the benefits and importance of alewife restoration. NFWF has 

indicated to DMR that they are interested in funding a two-year outreach position. The 

successful candidate will work on an outreach plan and develop educational materials 

(i.e. that can be used at meetings, schools, public speaking engagements, in blogs and 

chat rooms, at outdoor shows, the Penobscot River Festival, left at Chamber of 

Commences, press release, etc) and enlist members of the public to assist with 

outreach. 

Comment: There needs to be more on economics in this plan from multiple aspects, 

including costs and benefits. 

Response: The agencies involved in this operational plan are responsible for fisheries 

management. One of the strategies (29) was to enlist the interest and collaboration of 

experts in human dimensions, to evaluate the economics related to anadromous fish 

restoration, including costs and benefits. Further, we use human dimensions to include 

all levels of society, including communities (see page 104). 

Appendices: 

Comment: Appendix E should be expanded to include a discussion of the management 

alternatives for alosine restoration (e.g., natural recovery, use of in-basin adult transfers, 

use of out-of-basin fish transfers, hatchery culture), the pros and cons of each 

alternative, and a description of why an alternative may or may not meet the restoration 

objective. 

Response: Appendix E was meant to address the complex options available for Atlantic 

salmon management. We do not feel the inclusion of other species management 

options is appropriate. Appendix A discusses management approaches for alosines. 

PRFP Page 351

Comment: Plan often uses the terms self-sustaining and sustainable without a clear 

definition 

Response: We will replace the term “sustainable” with the term “self-sustaining” 

throughout the document for clarity and consistency. We will insert this definition for 

self-sustaining: “A population that exists in sufficient numbers to replace itself through 

time without supplementation with hatchery fish. It does not necessarily produce surplus 

fish for harvest. Self-sustaining diadromous populations spawn in the wild, and migrate 

to and from the ocean with a minimum of human interference.” 

Target population levels meet the definition of self-sustaining based on empirical 

experience, theory, and modeling. We used these information sources as available to 

establish target population levels. Where target populations levels are specified, we 

believe these levels will result in self-sustaining populations. However, establishing 

self-sustaining population levels a priori has been one of the greatest challenges of 

conservation biology, and we do not propose to solve this challenge in this plan. The 

levels set are our best estimate of what will be needed to achieve self-sustaining status. 

To move beyond this, involved population dynamics modeling, such as PVA, would be 

required to estimate the probability of achieving self-sustaining status under various 

scenarios. However, such modeling is only as good as the assumptions and data used 

to build the model(s). 

Others: 

Comment: What happens when alewives are leaving - will it impact bait seiners? 

Response: We asked the IFW regional offices for information. Region A didn’t recall 

any complaints but suspects the bait dealers may have simply learned to avoid the 

situation. Region B had a complaint about anadromous alewives migrating the fall in the 

Sebasticook River. Region C is not aware of dealers who spend any time seining for 

bait when the juvenile alewives are on the shore. 

Comment: What fishing regulations might be put in place below Milford Dam when it is 

the first dam on the river? 

Response: The same 150 foot closure below the fishway (already in place) will remain 

and the closure below the Veazie Dam will be revisited. 

Comment: The placement of size limits in Schoodic for LLS is a concern. 

Response: This question has less to do with the diadromous fish plan and more to do 

with the Atlantic salmon ESA listing, and potential impacts to recreational fishing. MIFW 

manages Schoodic Lake as a trophy landlocked salmon water, and plans to do so in the 

future. The 25-inch maximum length limit for landlocked salmon that is in place for the 

Downeast salmon rivers as well as the mainstem Penobscot River that protects 2SW 

sea-run Atlantic salmon in areas where incidental take may occur, would severely 

hamper the trophy landlocked salmon program at Schoodic Lake. Currently DMR does 

not place a high value on Schoodic Lake nor its’ tributaries with regard to sea-run 

Atlantic salmon production. 

PRFP Page 352

Comment: Several people commented that the money needed to carry out this plan 

could be better spent. 

Response: The missions of DMR, to conserve, manage and restore diadromous fish 

populations to Maine’s rivers, and of IFW to conserve, protect and enhance the inland 

fisheries and wildlife resources, are the reasons why we developed this plan. No 

money has been earmarked for this plan. 

Comment: Several people commented that the plan protects most of the resources and 

is a balance between protection and restoration and is ambitious, extensive, complete, 

ecosystem-based, and holistic. 

Response: Thank you 

Comment: Many comments were about the PRRP and not the fisheries plan. 

Response: There are other avenues to express concerns or support for the PRRP as 

the project goes through permitting. All notices regarding this project are placed in 

Bangor Daily News. 

Recommended Changes to POP 

1. More information on the shad model will be added as an appendix 

2. The shad and alewife sections will be clarified – particularly that Sebec, Seboeis 

and Schoodic are all Phase 3 lakes and to clarify that in basin stocks will be used 

first if the funding is available. 

3. Staff will have a discussion about the substitution of “safe, timely, and effective” 

for efficiency standards in the passage section. 

4. The four MOUs will be finalized and added as Appendices 

5. Additional references will be added to the habitat section 

6. A task will be added to Objective 27 that reads: Develop an outreach strategy 

that incorporates the tasks that follow and identifies additional ways to educate 

the general public on the benefits and importance of alewife restoration. 

7. The pike group will meet and review the habitat model results and use best 

professional judgment to re-classify risk to lakes and this will be added to the 

plan. 

8. We will replace the term “sustainable” with the term “self-sustaining” throughout 

the document for clarity and consistency. We will insert this definition for selfsustaining: 

“A population that exists in sufficient numbers to replace itself through 

time without supplementation with hatchery fish. 

9. Work plan tables will be consistent with costs and staff needs 

10. Lead authors for each section and appendices 

11. Add Atlantic salmon strategic objectives as an Appendix 

12. Fix spelling and formatting errors 

13. Remove Section 6 as it is internal to DMR 

14. Clarify that we will update but not re-write the plan and budget in 5 years 

15. The response to comments will be added to the end of the plan. 

PRFP Page 353

Operational Plan for the Restoration of Diadromous Fishes to the ...

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