Tuolumne River Report - U.S. Fish and Wildlife Service


Tuolumne River Report - U.S. Fish and Wildlife Service

Habitat Restoration Plan for theLower Tuolumne River CorridorPrepared for:The Tuolumne River Technical Advisory CommitteeMarch 2000

Front cover photographs (clockwise from top-left)• Adult chinook salmon returning to the river to spawn• A dynamic gravel bar near Basso Bridge at river mile 49.2• La Grange Dam at river mile 52.2• Mature valley oak and Fremont cottonwood riparian forest


TABLE OF CONTENTSTABLE OF CONTENTSLIST OF FIGURES ........................................................................................................ viiLIST OF TABLES ............................................................................................................ xiTABLE OF CONTENTSACKNOWLEDGMENTS ............................................................................................... xiiiLIST OF AUTHORS AND CONTRIBUTORS .............................................................. xiiiPREFACE ....................................................................................................................... xvEXECUTIVE SUMMARY.............................................................................................. xviiChapter 1. INTRODUCTION ........................................................................................ 11.1. GEOGRAPHICAL SETTING .........................................................................................11.2. PRECURSORS TO THIS RESTORATION PLAN ..........................................................21.3. CLARIFICATION OF TERMINOLOGY ..........................................................................51.3.1. Restoration vs. Rehabilitation ............................................................................................... 51.3.2. Historical salmonid populations ............................................................................................ 51.3.3. Ecosystem-based approach to restroation ........................................................................... 61.4. SCOPE OF THE RESTORATION PLAN .......................................................................71.4.1. Corridor versus watershed boundaries ............................................................................. 71.4.2. Focus on natural chinook salmon production ................................................................... 71.5. OBJECTIVES ..............................................................................................................8Chapter 2. LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORY ..... 112.1. HYDROLOGY ............................................................................................................ 122.1.1. The unimpaired flow regime ............................................................................................ 122.1.2. Regulated flow regime .....................................................................................................232.2. FLUVIAL GEOMORPHOLOGY .................................................................................. 272.2.1. Fluvial geomorphic process ............................................................................................. 272.2.2. Geomorphic reach delineation ........................................................................................ 292.2.3. Channel morphology (cross section and planform) ....................................................... 312.3. ATTRIBUTES OF ALLUVIAL RIVER ECOSYSTEM INTEGRITY ................................. 382.4. BIOLOGICAL RESOURCES ...................................................................................... 452.4.1. Riparian resources .......................................................................................................... 452.4.2. Chinook salmon ............................................................................................................... 562.4.3. Fish and wildlife resources .............................................................................................. 732.5. SUMMARY ................................................................................................................ 73Chapter 3. GEOMORPHIC AND RIPARIAN INVESTIGATIONS ............................... 773.1. FLUVIAL PROCESSES .............................................................................................783.1.1. Bedload impedance reaches (Attribute #5) ......................................................................... 783.1.2. Bed mobility thresholds (Attribute #3) ................................................................................. 793.1.3. Bedload transport (Attribute #5) .......................................................................................... 843.1.4. Fine sediment sources (Attribute #5) .................................................................................. 873.1.5. M.J. Ruddy 4-Pumps restoration project evaluation ............................................................ 913.1.6. Channel design considerations .......................................................................................... 93iii

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORTABLE OF CONTENTS3.2. FLOOD FLOW EVALUATION ..................................................................................... 953.2.1. Fluvial geomorphic thresholds ........................................................................................ 953.2.2. Feasibility of using flood management or power peaking releases to improvefluvial processes ............................................................................................................. 1073.2.3. Constraints ...................................................................................................................... 1093.3. AGGREGATE SOURCE INVENTORY ...................................................................... 1143.3.1. Special Report 173........................................................................................................... 1143.3.2. McBain & Trush inventory ................................................................................................. 1153.3.3. Summary ......................................................................................................................... 1213.4. RIPARIAN EVALUATION ......................................................................................... 1223.4.1. Tuolumne River Riparian inventory ................................................................................... 1223.4.2. Description of riparian vegetation in Sand-bedded Zone .............................................. 1263.4.3. Description of riparian vegetation in Gravel-bedded Zone ............................................ 1273.4.4. Riparian vegetation relationships to contemporary and historic fluvial geomorphology ...... 1293.4.5. Summary ......................................................................................................................... 1413.4.6. Riparian limiting factors .................................................................................................... 1413.4.7. Recommendations........................................................................................................... 142Chapter 4. RESTORING THE TUOLUMNE RIVER CORRIDOR ........................... 1434.1. RESTORATION GOALS AND OBJECTIVES ............................................................ 1434.1.1. Goals and objectives of existing restoration programs ...................................................... 1434.1.2. New Don Pedro Project FERC Settlement Agreement ..................................................... 1444.1.3. River-wide restoration goals ............................................................................................. 1454.2. RESTORATION STRATEGIES ................................................................................. 1474.2.1. Sand-Bedded Zone ........................................................................................................ 1474.2.2. Gravel-Bedded Zone ...................................................................................................... 1474.3. RESTORATION AND PRESERVATION APPROACHES .......................................... 1504.3.1. Preservation sites ........................................................................................................... 1504.3.2. Floodway expansion ....................................................................................................... 1504.3.3. Riparian restoration strategies ...................................................................................... 1514.3.4. Channel reconstruction .................................................................................................. 1544.3.5. Fine sediment (sand) management .............................................................................. 1554.3.6. Coarse sediment (spawning gravel) management ...................................................... 1554.3.7. Microhabitat restoration ..................................................................................................1564.3.8. Miscellaneous ................................................................................................................ 1574.4. RESTORATION SITE IDENTIFICATION AND SELECTION ....................................... 1574.5. SUMMARY OF 14 CHANNEL RESTORATION PROJECTS ..................................... 1594.5.1. Special Run Pool 5 Channel Restoration Project ......................................................... 1594.5.2. Special Run Pool 6 Channel Restoration Project ......................................................... 1604.5.3. Special Run Pool 9 Channel Restoration Project ......................................................... 1614.5.4. Special Run Pool 10 Channel Restoration Project ....................................................... 1624.5.5. Gravel Mining Reach Channel Restoration Project (Four phases) ............................... 1634.5.6. Tuolumne River Sediment Management and Implementation Plan ............................. 1654.5.7. Dredger Tailing Reach Channel Restoration Project (Three phases) .......................... 1664.5.8. Basso Spawning Reach floodplain restoration (RM 47.6 to 50.5) ................................ 167iv

TABLE OF CONTENTSChapter 5. ADAPTIVE MANAGEMENT ..................................................................... 1715.1. MONITORING .......................................................................................................... 1725.2. RIVER-WIDE MONITORING PROTOCOLS ............................................................. 1735.3. FERC SETTLEMENT AGREEMENT CHINOOK SALMON MONITORING ................. 1765.3.1. River-wide monitoring (FSA Section 13) ........................................................................... 1765.3.2. Site-specific monitoring objectives ................................................................................... 1775.3.3. Summary of completed, ongoing, and proposed monitoring efforts(in addition to FSA section 13) .......................................................................................... 1775.3.4. Summary ........................................................................................................................ 178TABLE OF CONTENTSREFERENCES ............................................................................................................. 179APPENDICESAppendix A. Annual Hydrographs for the Tuolumne River at La Grange ................................... 185Appendix B. Tuolumne River Series Lists, Species Lists, and Riparian Inventory Map ........... 207Appendix C. CD Rom Containing Field Data, Riparian Inventory Maps, and PDF Versionsof Restoration Planv


LIST OF FIGURESChapter 1Figure 1-1. Location of the lower Tuolumne River, Stanislaus County, California ............................. 1Figure 1-2. Tuolumne River downstream of the New Don Pedro Project (NDPP) showing urbanareas, tributaries, TID/MID regulation facilities, and major roads. .................................. 2Figure 1-3. Major streamflow diversion structures and volumes of water diverted from theTuolumne River basin (water volumes are 1984-1998 averages). .................................... 3Figure 1-4. Timeline of specific actions required by the FERC Settlement Agreement. ..................... 4Figure 1-5. Different states of ecosystem recovery based on change in ecosystem structure andfunction (modified from Bradshaw 1984). ........................................................................ 5LIST OF FIGURESChapter 2Figure 2-1. Tuolumne River at La Grange annual hydrograph for WY 1979(NORMAL water year type) to illustrate hydrograph components. ................................ 13Figure 2-2. Annual unimpaired water yield for the Tuolumne River at La Grange,from WY 1897 to 1999. ................................................................................................... 14Figure 2-3. Cumulative plot of ranked annual water yields for the Tuolumne River atLa Grange, showing exceedence probabilities of annual yield and wateryear classification scheme. ............................................................................................... 15Figure 2-4. Average and representative (WY 1967) EXTREMELY WET water year annualhydrographs for the Tuolumne River at La Grange. ....................................................... 16Figure 2-5. Average and representative (WY 1940) WET water year annual hydrographsfor the Tuolumne River at La Grange. ............................................................................. 16Figure 2-6. Average and representative (WY 1946) NORMAL water year annualhydrographs for the Tuolumne River at La Grange. ....................................................... 17Figure 2-7. Average and representative (WY 1985) DRY water year annualhydrographs for the Tuolumne River at La Grange. ....................................................... 17Figure 2-8. Average and representative (WY 1987) CRITICALLY DRY water year annualFigure 2-9.hydrographs for the Tuolumne River at La Grange. ....................................................... 18Annual maximum flood frequency curves for unimpaired and post-NDPPperiods at La Grange. ....................................................................................................... 22Figure 2-10. Tuolumne River at La Grange, unimpaired annual hydrographs during snowmeltrecession for each water year class, and the 1971-1997 average hydrograph for theimpaired post-NDPP period. ............................................................................................ 23Figure 2-11. Daily average flow duration curves for unimpaired and post-NDPP periods atLa Grange. ........................................................................................................................ 24Figure 2-12. Tuolumne River at La Grange annual hydrograph of unimpaired streamflowand post-NDPP streamflow for WY 1994 (DRY water year type), showingchanges in hydrograph components from unimpaired conditions. ................................. 27Figure 2-13. Conceptual flow-sediment balance necessary for channel equilibrium, andchannel response to disequilibrium.................................................................................. 28Figure 2-14. Tuolumne River geomorphic reach delineation............................................................... 30Figure 2-15. Tuolumne River water surface profiles generated by the 1969 USGSchannel capacity study. ..................................................................................................... 32Figure 2-16. Idealized alternate bar unit, modified from Dietrich (1987)and McBain and Trush (1997). . ...................................................................................... 34Figure 2-17. 1937 example alternate bar sequence in sand-bedded reach near theSan Joaquin River confluence (RM 4.5). .........................................................................36Figure 2-18. 1937 example alternate bar sequence in sand-bedded reach immediatelydownstream of the gravel-to-sand bedded transition (RM 23). ........................................ 37Figure 2-19. 1937 example alternate bar sequence in gravel-bedded reach, near 7/11Materials plant site at RM 38. ........................................................................................... 38vii

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR LIST OF FIGURESLIST OF FIGURESFigure 2-20. Cross section at RM 35.5 showing fossilized pre-NDPP bankfull channeland floodplain surface in gravel-bedded reach. ...............................................................39Figure 2-21. 1993 example alternate bar sequence in gravel-bedded reach, (RM 38). .......................41Figure 2-22. 1950 photo of dredger tailings upstream of Roberts Ferry (RM 43). ............................42Figure 2-23. 1993 example alternate bar sequence in sand-bedded reach near theSan Joaquin River confluence (RM 4.5). .........................................................................43Figure 2-24. 1993 example alternate bar sequence in sand-bedded reach immediatelydownstream of the gravel-to-sand bedded transition (RM 23). ......................................44Figure 2-25. A generalized riparian hardwood life cycle showing life stages andmortality agents that affect life stages. ............................................................................47Figure 2-26. Conceptual role of channel migration in creating spatially and temporallycomplex riparian corridor habitat. ...................................................................................48Figure 2-27. 1937 photo near the confluence of the San Joaquin River, showing oxbowsand scroll-bars, bank erosion, and the range of riparian age classes. ..............................49Figure 2-28. Conceptual historical cross-section near Shiloh Bridge (RM 3.5). ...............................50Figure 2-29. Riparian corridor widths in 1937 and 1993, starting at the TuolumneRiver’s confluence with the San Joaquin River (RM 0.0) and endingjust upstream of the New La Grange Bridge (RM 51.5). ................................................53Figure 2-30. Conceptual existing cross-section near Shiloh Bridge (RM 3.5). ..................................54Figure 2-31. Life cycle of the Tuolumne River fall-run chinook salmon showing how majorstages in their life history relate to typical annual runoff patterns. ................................56Figure 2-32. Conceptual cross section through a spawning riffle to show the effects of flowvariation on distributing spawning area to lateral margins of the channel. .....................59Figure 2-33. Daily average flows during chinook salmon spawning season (Oct 1-Dec 20) forunimpaired water years 1947-1956, and for Regulated water years 1973-1982. ..........60Figure 2-34. Magnitude and timing of the first fall storms of each water year of record,showing minimal differences between waer year classes. ..............................................61Figure 2-35. Historical chinook salmon escapements, showing trends in populationbooms and crashes. ...........................................................................................................63Figure 2-36. Idealized alternate bar sequence showing location of habitat featuresused by chinook salmon. ..................................................................................................64Figure 2-37. Location of salmon redds in riffle 3A (RM 49.4), showing use of riffle andpool tail habitat for spawning, and a preference for lateral (margin) zones....................66Figure 2-38. Aerial photograph from March 1950, showing the alternate barsequence at RM 38.0. .......................................................................................................67Chapter 3Figure 3-1.Figure 3-2.Typical bedload impedance reach, where instream aggregate extraction pittraps all bedload transported from upstream reaches. .....................................................78Location of tracer rock experiments and bed mobility modeling in thegravel-bedded zone, Tuolumne River. ..............................................................................81Figure 3-3. Tuolumne River at La Grange streamflows during tracer rock experiments. ................82Figure 3-4. Delineation of total sediment load generated from a given watershed. ..........................87Figure 3-5. M.J. Ruddy reach data collection sites (RM 34.6 to 37.6). ............................................95Figure 3-6. M.J. Ruddy mitigation site, Cross section 60+61. ..........................................................96Figure 3-7. M.J. Ruddy 4 Pumps site, Cross section 67+53. ............................................................96Figure 3-8. M.J. Ruddy 4 Pumps site, Cross section 79+61. ............................................................97Figure 3-9. M.J. Ruddy 4 Pumps site, Cross section 88+10. ............................................................97Figure 3-10. M.J. Ruddy 4 Pumps site, Cross section 94+97. ............................................................98Figure 3-11. M.J. Ruddy 4 Pumps site, Cross section 99+14. ............................................................98Figure 3-12. M.J. Ruddy 4 Pumps site, Cross section 107+71. ..........................................................99Figure 3-13. Tuolumne River 1996 longitudinal profiles from river mile RM 34.6 to 37.8. .............99Figure 3-14. Thalweg and water surface profiles through the M.J. Ruddy 4-Pumpsrestoration site, RM 36.8 to 37.7. ................................................................................ 100viii

Figure 3-15. Natural two-stage channel (A), and impact of encroached channel, (B),and unconfined channel, and (C) on shear stress and bedload transport. ..................... 101Figure 3-16. Shear stress distribution on Trinity River cross sections confinedby riparian encroachment............................................................................................ 102Figure 3-17. Shear stress distribution on Trinity River cross sectionsin unconfined restored reaches. .................................................................................... 102Figure 3-18. Cross section survey at Old La Grange Bridge (RM 50.5) showing channeldowncutting resulting from the January 1997 flood (60,000 cfs). .............................. 103Figure 3-19. Cross section at New La Grange Bridge (RM 49.9) showing channeldowncutting resulting from January 1997 flood (60,000 cfs). .................................... 104Figure 3-20. Longitudinal profiles of Tuolumne River downstream of Old BassoBridge before and after the January 1997 flood (60,000 cfs),illustrating scour and loss of riffles due to channel confinement. .............................. 105Figure 3-21. Conceptual evolution of pool-riffle morphology in confined reachesof the Tuolumne River. .................................................................................................. 106Figure 3-22. Tuolumne River annual hydrograph for 1970 with hypothetical hydrographmodifications to improve geomorphic processes. ........................................................ 110Figure 3-23. Tuolumne River annual hydrograph for 1980, with hypothetical hydrographmodifications to improve geomorphic processes. ........................................................ 110Figure 3-24. Tuolumne River annual hydrograph for 1982, with hypothetical hydrographmodifications to improve geomorphic processes. ........................................................ 111Figure 3-25. Tuolumne River annual hydrograph for 1983, with hypothetical hydrographmodifications to improve geomorphic processes. ........................................................ 111Figure 3-26. Tuolumne River annual hydrograph for 1984, with hypothetical hydrographmodifications to improve geomorphic processes. ........................................................ 112Figure 3-27. Tuolumne River annual hydrograph for 1986, with hypothetical hydrographmodifications to improve geomorphic processes. ........................................................ 112Figure 3-28. Tuolumne River annual hydrograph for 1995, with hypothetical hydrographmodifications to improve geomorphic processes. ........................................................ 113Figure 3-29. Tuolumne River annual hydrograph for 1996, with hypothetical hydrographmodifications to improve geomorphic processes. ........................................................ 113Figure 3-30. Aggregate resource areas and permitted reserves identified on theTuolumne River by Higgins and Dapras (1993) between RobertsFerry (RM 40) and La Grange Dam (RM 52). ............................................................... 116Figure 3-31. Gravel inventory sites identified on the Tuolumne River between RobertsFerry (RM 40) and La Grange Dam (RM 52). ............................................................... 118Figure 3-32. Gravel inventory sites identified in the Merced River dredger tailings, nearSnelling CA. ....................................................................................................................119Figure 3-33. Basso Bridge vegetation transect location (RM 47.0). ................................................ 131Figure 3-34. Santa Fe vegetation transect location (RM 22.5). ........................................................ 132Figure 3-35. Confluence vegetation transect location (RM 0.5). ..................................................... 133Figure 3-36. Cross section survey and location of riparian vegetation at BassoBridge vegetation transect (RM 47.0). ......................................................................... 134Figure 3-37. Basso Bridge vegetation transect (RM 47.0). .............................................................. 135Figure 3-38. Relationship of cottonwood and valley oak trunk diameters to rootingelevations at Zanker model transect. ............................................................................ 136Figure 3-39. Cross section survey and location of riparian vegetation at Santa Fevegetation transect (RM 22.5). ..................................................................................... 137Figure 3-40. Photographs of Santa Fe vegetation transect (RM 22.5).............................................. 138Figure 3-41. Cross section survey and location of riparian vegetation at Confluencevegetation transect (RM 0.5). ...........................................................................................139Figure 3-42. Photographs of Confluence vegetation transect (RM 0.5). ..............................................140LIST OF FIGURESix

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR LIST OF FIGURESLIST OF FIGURESChapter 4Figure 4-1. Geomorphic reach delineation and proposed restoration strategiesfor the lower Tuolumne River. ...................................................................................... 148Figure 4-2. Proposed modification to berm confined channel morphology toimprove flood conveyance and reduce habitat damage during floods. ......................... 152Figure 4-3. Proposed modification to riparian and/or agriculturally encroachedchannel morphology to improve flood conveyance and reduce habitatdamage during floods. ................................................................................................... 152Figure 4-4. Recommended restoration strategy for straight, converting incised channelto natural alternate bar sequence with two stage channel. ............................................ 153Figure 4-5. Conceptual restored floodway, with bankfull channel, floodplains, and terraces. ....... 154Figure 4-6. Suggested “gravel transfusion” insertion method to quickly restore andreplenish instream alluvial deposits. ............................................................................. 156x

LIST OF TABLESLIST OF TABLESChapter 2Table 2-1. Tuolumne River at La Grange annual water yield and water yieldclassification for unimpaired and post-NDPP regulated conditions. .............................16Table 2-2. Important components of annual unimpaired hydorgraphs of daily averageflow for the Tuolumne River at La Grange, analyzed for five differentwater year classes. ............................................................................................................20Table 2-3. Tuolumne River at La Grange pre- and post-NDPP annual maximum seriesflood frequency data. ........................................................................................................21Table 2-4. Minimum flow releases from NDPP as required by Article 37 of the originalFERC License...................................................................................................................25Table 2-5. Revised minimum flow releases from NDPP required by FERC LicenseArticle 37 amendment (1995 to present). .......................................................................26Table 2-6. Land uses and effects on the lower Tuolumne River from 1849 to present. ..................40Table 2-7. Relationships between established riparian plant series, flood frequency,and streamflow for the lower Tuolumne River corridor. .................................................52Table 2-8. Major impacts to chinook salmon habitat and population levels resulting fromalterations to the historical hydrologic and fluvial geomorphic processes. ...................58Table 2-9. Comparison of estimated riffle and spawning areas from 1950 photos withcontemporary (1986) conditions in the Tuolumne River Corridor. ................................69Table 2-10. Fishes of the lower Tuolumne River observed since 1981 inTID/MID fishery studies ..................................................................................................74Chapter 3Table 3-1. Bedload routing impedance reaches on the Tuolumne River...........................................78Table 3-2. Insertion location, quantity, and size range of tracer rocks on the Tuolumne River. ......79Table 3-3. Hydraulic characteristics of selected high flows observed on the TuolumneRiver in WY 1996 and 1997, with tracer rock results. ................................................... 83Table 3-4. Summary table of 1997 bedload transport measurements. ............................................. 85Table 3-5. Potential fine sediment point sources between RM 32 and RM 52. ..............................89Table 3-6. Particle size distribution summary for Tuolumne River pebble countscollected in summer 1996. ..............................................................................................92Table 3-7. Water years 1995 to 1997 flood histories at the Tuolumne River at LaGrange gaging station. ......................................................................................................93Table 3-8. Water years 1970-1997 instream releases, and potential modifications topeak flows to improve geomorphic processes. ............................................................ 108Table 3-9. Summary of upper Tuolumne and Merced River aggregate source inventory. ............. 120Table 3-10. Total surface area of riparian vegetation series within the lower TuolumneRiver corridor. ............................................................................................................... 124LIST OF TABLESxi


ACKNOWLEDGMENTSACKNOWLEDGMENTSThis Habitat Restoration Plan for the Lower Tuolumne River Corridor has, in actuality, been in the makingduring the past three decades since the New Don Pedro Project was completed in 1971. During this time,numerous scientists, ranging from resource agency personnel and river restoration specialists to studentfield technicians, have contributed endless hours of labor gathering information and contributing theirknowledge on river and salmon ecology, fluvial and hydrologic processes, insights on site-specificconditions, and management strategies along the 52 mile river corridor. This considerable effort wasmade in the name of restoring the Tuolumne River, saving the chinook salmon population, and protecting avalued resource that will be passed along to future generations. Our connected legacy lies in the successof our efforts.We have attempted to synthesize the relevant information that was available to describe the historical andcontemporary river conditions into a unified, refined restoration strategy. This culmination would nothave been possible without many individuals who contributed directly or indirectly to this report. Themembers of the Tuolumne River Technical Advisory Committee (TRTAC), many of whom were involvedin negotiating the 1995 FERC Settlement Agreement, deserve foremost recognition for their cooperationand shared vision toward the goal of improving the Tuolumne River ecosystem. Of the many technicalcommittees with whom we’ve worked, the TRTAC has been the most collegial, knowledgeable, andprofessional of them all.The TRTAC members also contributed to the content of the Restoration Plan by providing several valuablereviews and edits of the draft Restoration Plan. Several local landowners have contributed to this reportand restoration process, including the Warner family, Will Streeter, Walt Deardorff, the Sawyer family,Joe Ruddy, the Hall family, Paul Von Konynenburg, and the Zanker family, among others. The City ofModesto and Stanislaus County Regional Planners deserve mention for their efforts to incorporate theirvision for the Tuolumne river Regional Park into a long-term vision for the entire community. CarolVierra, Joe Ruddy, Bill Brown, and Ron Turcott have contributed to making the Gravel Mining Reachrestoration project possible.The Tuolumne River has been particularly fortunate in receiving generous funding support from severalsources, including: the Turlock and Modesto Irrigation Districts, City and County of San Francisco, theAnadromous Fish Restoration Program, CALFED, and the Natural Resources Conservation Service.Numerous individuals helped gather field data and provide input for this document, including GretchenHayes, Timothy Ramirez, Graham Matthews, Jennifer Vick, Wesley Smith, and Aldaron Laird. KevinFalkenberry of DWR contributed to valuable discussions about the M.J. Ruddy Restoration Project andchannel design concepts. Frank Ligon provided the original inspiration for developing the RestorationPlan, and later discussions provided valuable improvements in the document.ACKNOWLEDGMENTSLIST OF AUTHORS AND CONTRIBUTORSMcBain and TrushScott McBainDarren MierauJohn BairDr. William TrushRebecca McBainTara KoehlerFred MeyerBrian MerrillGretchen HayesTurlock Irrigation DistrictWilton FryerTim FordRoger Masudaxiii


PREFACEPREFACEThe Tuolumne River is one of the most importantnatural resources of California’s Great CentralValley. The largest tributary of the San JoaquinRiver, the Tuolumne River drains a 1,900 squaremilewatershed that includes the northern half ofYosemite National Park. As the Tuolumne Riveremerges from the Sierra Nevada foothills into theCentral Valley, it carries precious agricultural andmunicipal water supplies to a highly developedand diversified regional economy. Agriculture,ranching, mining, and tourism dominate theregion and depend on the river for their sustainedlivelihoods.An enormous biological community also dependson the Tuolumne River. Vast Fremont cottonwoodand Valley Oak riparian forests once insulated theTuolumne River banks, extending several mileswide in the lower San Joaquin Valley, and merginginto riparian forests of the neighboring Merced,Stanislaus and San Joaquin rivers. These forestsprovided foraging and breeding habitat for adiverse array of resident and migratory bird andwildlife populations, including tremendouspopulations of migratory waterfowl. Despite recentdeclines, the Tuolumne River still supports thelargest naturally reproducing population ofchinook salmon remaining in the San JoaquinValley.The Turlock Irrigation District (TID) and theModesto Irrigation District (MID), which ownand operate the New Don Pedro Dam andReservoir and La Grange Dam, and provide waterand electricity to much of Stanislaus County, havea legal and historic role as stewards of the LowerTuolumne River. Sharing in this responsibility asstewards of the Tuolumne River’s natural resourcesare regulatory agencies and stakeholders,including several state and federal resourceagencies, public utilities, and private organizations.This group includes TID, MID, California Departmentof Fish and Game (CDFG), US Fish andWildlife Service (USFWS), the Federal EnergyRegulatory Commission (FERC), the NationalMarine Fisheries Service (NMFS), the City andCounty of San Francisco (CCSF), San FranciscoBay Area Water Users Association (BAWUA),Friends of the Tuolumne (FOTT), the TuolumneRiver Preservation Trust (TRPT), Tuolumne RiverExpeditions (TRE), and California Sports FishingProtection Alliance (CSFPA).The Tuolumne River stakeholders entered into anhistorical agreement in 1995, following re-evaluationof the original FERC license for the New DonPedro Project (NDPP). This historic agreement,known as the 1995 FERC Settlement Agreement(Settlement Agreement or FSA) establishedseveral important strategies for reversing thedecline of fall-run chinook salmon in the lowerTuolumne River: (1) higher minimum instream flowrequirements below La Grange Dam, (2) expandedchinook salmon monitoring program, (3) developmentand implementation of a lower TuolumneRiver chinook salmon habitat restoration program,and (4) salmon management and habitat restorationactivities coordinated and administeredthrough a Tuolumne River Technical AdvisoryCommittee (TRTAC), composed of the stakeholderorganizations.A central directive of the FERC Settlement Agreementwas to identify and implement ten priorityhabitat restoration projects by the year 2005, atwhich time FERC would evaluate progress towardSettlement Agreement objectives. As part of thisprocess to identify and implement ten priorityrestoration projects, the TRTAC has commissionedfisheries habitat restoration scientists to develop a“Habitat Restoration Plan for the Lower TuolumneRiver Corridor” (Restoration Plan).The Restoration Plan will be used by the TRTAC tohelp fulfill its obligations to the FERC under the1995 Settlement Agreement. The Restoration Planis a technical resource document intended to aid inidentifying areas of potential habitat improvementand provide guidance for restoring or rehabilitatingthese areas. The Plan is not intended to supercederegulatory agency management obligations andpreviously developed restoration plans (e.g.,CDFG 1990, 1992, CVPIA/AFRP 1995, CALFEDERPP 1999, and CALFED Strategic Plan 1998), butinstead is intended to provide additional technicalinformation to the TRTAC for use in makingrestoration decisions.Implementation of any specific habitat restorationproject will be subject to prior environmentaldocumentation and review as required by stateand federal regulations (California EnvironmentalQuality Act; National Environmental Policy Act).Selected projects will be subject to pre-projectplanning discussions with affected landownersother interested public entities, along withPREFACExv

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORPREFACEparticipation from applicable federal, state, andlocal regulatory agencies. Restoration activitiesmay include the transfer of private lands, mineralrights, water rights, etc., through purchase,conservation easement, or other means. Participationin restoration activities by landowners andother members of the public is entirely voluntary.The TRTAC stakeholders understand thatdecisions affecting the lower Tuolumne River areinfluenced by policies relating to land use, watersupply and use, water quality, flood control, fishand wildlife, and recreation, and are not governedsolely by physical habitat considerations.The Tuolumne River Technical Advisory Committeexvi

EXECUTIVE SUMMARYEXECUTIVE SUMMARYPrior to major human settlement and land developmentin the Great Central Valley of California, thelower Tuolumne River was a dynamic, meanderingalluvial river, with broad floodplains and terraces,large gravel bar deposits, and extensive riparianwetlands and forests harboring a rich diversity ofspecies. An alluvial river has riverbed, banks, andfloodplains composed of coarse and fine sediments(sand, gravel, and cobble) that were eroded,transported, and deposited by the forces ofrunning water. A natural river is dynamic, havingthe ability to frequently move the channelbed andbanks, scour coarse sediments and transport themdownstream, to be replaced by comparable materialtransported from upstream. In this way, themorphology or shape of the river channel ismaintained in a state of “dynamic quasi-equilibrium”over time. This condition provides thephysical foundation of the riverine ecosystemupon which native plant and animal communitiesdepend for their survival. Native flora and faunaevolved within this natural riverine environment.Alteration of this physical environment, as hasoccurred extensively on the Tuolumne River, hasadversely impacted the native salmon fisheryalong with associated plant and animal communities.The fundamental premise of this Restoration Planis that a dynamic, healthy river ecosystem can berestored on the Tuolumne River if the fluvialgeomorphic and hydrologic processes that createand maintain the physical landscape are restored.River ecosystems are extremely complex; fluvialgeomorphic and hydrologic processes sustain analluvial river’s structure and function. Therefore,improving natural processes within the constraintsof present-day flow conditions, sedimentsupply, and land use must be an integral strategyfor restoring and managing the Tuolumne River.While advocating this fundamental premise, weacknowledge that restoration actions cannot beexpected to return the Tuolumne River to historicalconditions that existed prior to modernsettlement and intensified land development ofthe region. Instead, physical processes areintended to be used as tools for creating andmaintaining habitat, in accordance with othermanagement strategies. Success of this approachis fundamentally dependent on adaptive managementtechniques to evaluate restoration opportunities,the efficacy of actions and approaches, andthen redirect strategies if needed. The TuolumneRiver Technical Advisory Committee (TRTAC) willbe the focus of this process.The purpose of each chapter in this RestorationPlan is as follows:• CHAPTER 1: Provide background informationdescribing the need to develop a technicallybasedRestoration Plan;• CHAPTER 2: Integrate salmon ecology andmanagement with contemporary knowledge offluvial geomorphic and hydrologic processes todevelop an ecosystem-based restorationstrategy;• CHAPTER 3: Conduct and present results offluvial geomorphic and riparian investigationsthat evaluated contemporary fluvial geomorphicprocesses, riparian conditions, and potentialaggregate sources for restoration purposes;• CHAPTER 4: Integrate this information topresent river-wide and reach-specific restorationgoals and strategies, a comprehensive listof all potential restoration sites and actions, andconceptual designs for fourteen high priorityrestoration projects;• CHAPTER 5: Develop an Adaptive EnvironmentalAssessment and Management (AEAM)approach that recommends river-wide and sitespecific monitoring objectives, guides futuremanagement, and ensures restoration andmaintenance of the fishery resources of theTuolumne River.Historical and Contemporary ConditionsHydrology. The streamflow hydrology of theTuolumne River has changed from unimpairedconditions due to the cumulative water storageand diversion projects in the watershed. Hydrologicanalyses of streamflow records from theUSGS gaging station at La Grange (Station 11-289650, immediately downstream of La GrangeDam) illustrates three basic trends in hydrologicalteration: (1) the annual water yield to the lowerTuolumne River below La Grange dam has beenprogressively reduced by dam regulation anddiversion, from an average annual unimpairedyield of 1,906,000 acre feet, to a post New DonPedro Project (NDPP) regulated annual yield of772,000 acre-feet, a 60% reduction in flowvolume; (2) specific “components” of the annualEXECUTIVE SUMMARYxvii

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOREXECUTIVE SUMMARYhydrograph, including summer and winterbaseflows, fall and winter storms, and springsnowmelt runoff have been reduced in all wateryear types from unimpaired conditions, includingreductions in magnitude and variability; (3) themagnitude, duration, and frequency of winterfloods have been reduced by regulation fromNDPP compared to unimpaired conditions; themean annual flood (based on annual maximumseries) has been reduced from 18,400 cfs to 6,400cfs; the 1.5-year recurrence event (approximatelybankfull discharge) has been reduced from 8,400cfs to 2,600 cfs; the 10-year recurrence event hasbeen reduced from 36,000 cfs to 9,500 cfs. Thisreduction in hydrology has, in turn, causedchanges to fluvial geomorphic processes, riparianvegetation, riverine habitats, and the biota thatuses these riverine habitats.Chinook Salmon. The fall-run chinook salmon isthe predominant anadromous salmonid run on theTuolumne River. Once thought to have numberedin the hundreds of thousands (including springrunchinook), chinook salmon have declined tosmall fractions of their previous numbers. Since1951, the Tuolumne River salmon population hasexperienced large fluctuations, ranging from 100to 45,000 spawners. The lowest San JoaquinBasin escapement of record occurred in 1963 withonly 300 spawners in the entire basin. TuolumneRiver escapements have plummeted from a highof 41,000 salmon in 1985 to 100 salmon in 1990,1991, and 1992. Salmon returns in recent years(1997-1999) have rebounded to near ten thousandadults.Several multi-year research programs conductedby the TID/MID, USFWS, and CDFG to assesschinook salmon population dynamics and habitatconditions on the Tuolumne River identifiedseveral “limiting factors” to chinook salmonproduction and survival. These factors included:• reduced spawning gravel quantity and quality,egg mortality from redd superimposition, andlow egg survival -to-emergence;• inadequate streamflow during fry and juvenileemigration;• reduced and degraded fry and juvenile rearinghabitat;• increased in-river predation by non-native fishspecies;• increased Bay/Delta and ocean mortality(predation, Delta pumping mortality, sport andcommercial harvest);• elevated in-river and Delta water temperatures.Many of these factors are related to degradation ofhabitat within the Tuolumne River corridor,which is in turn related to impaired fluvialgeomorphic processes, flow regulation, andphysical impacts from land use. The SettlementAgreement reverses some of these factors withimproved flows and physical habitat restorationefforts; however, the processes that create andmaintain habitat must still be incorporated intorestoration efforts.Riparian vegetation. Riparian corridors areuniquely dominated by winter-deciduous hardwoodtrees (e.g., cottonwood, willow, valley oak)which can only survive within the particularmicroclimatic and edaphic (soil moisture)conditions available within the river corridor. InCalifornia, the native amphibian, bird, andmammalian species diversity in Central Valleyriparian zones represents the highest biodiversityfound anywhere in the state (Tietje et at. 1991).Riparian zones support at least 50 amphibian andreptile species, 147 bird species, 55 mammalianspecies, and 60 native tree and plant species.The Tuolumne River riparian corridor is presentlya small remnant of historical conditions. TheRestoration Plan inventoried riparian vegetationwithin the entire Tuolumne River corridor usingthe plant series classification system developed bySawyer and Keeler-Wolf (1995). Of the 29riparian plant series identified, all native terrestrialvegetation series within the Tuolumne Rivercorridor are classified as “threatened” or “verythreatened”, with the exception of narrow-leafwillow and white alder. Dramatic losses of theselarge riparian stands has occurred from cumulativeimpacts of land uses, including agriculture,urban encroachment, aggregate mining, goldmining, and flow regulation. Riparian vegetationon the lower Tuolumne River is a composite ofrelic pre-NDPP vegetation on terraces, and post-NDPP vegetation on smaller recently built“floodplains”. Pre-NDPP vegetation reflects alarger hydrologic scale. This dramatic reductionin riparian vegetation, and the recognition thatriparian zones are biologically rich and thus vitalto river ecosystem integrity, have made riparianhabitat preservation and restoration highxviii

EXECUTIVE SUMMARYpriorities. Cottonwood and valley oak series areparticularly important overstory species, providinghabitat critical for birds (egrets, herons,osprey, bald eagles, and others). Dense understoryhabitat provided by willow and herbaceous plantsis important for wildlife such as rodents (includingthe endangered riparian brush rabbit), deer,and their predators.Fluvial Geomorphology. The lower Tuolumne Rivercorridor is divisible as two distinct geomorphiczones. The sand-bedded zone extends from RM 0.0to RM 24, and the gravel-bedded zone extendsfrom river mile 24 to 52.2. The corridor can befurther subdivided into seven distinct reachesbased on present and historical land uses. Thesehistorical land uses include:• placer mining for gold• dredger mining for gold• urban growth• livestock grazing• agriculture• streamflow regulation and diversion• commercial aggregate (gravel) miningThese disturbances have cumulatively degradedthe lower Tuolumne River ecosystem by:• decreasing the floodway capacity,• reducing or eliminating the low-flow andbankfull channel confinement,• degrading the channel morphology,• decreasing the frequency of large floods,• decreasing the variability of inter-annual andseasonal flows,• eliminating coarse sediment supply,• creating large in-channel and off-channelaggregate extraction pits,• reducing riparian vegetation coverage andstructural diversity,• increasing the distribution and abundance ofnon-native plant, fish, and wildlife species.The reduced quality of aquatic habitat is partlyresponsible for decreased chinook salmonescapement over the years. To begin reversingthese impacts and improving river ecosystemquality and chinook salmon populations, aframework is needed to guide restoration. Basedon interpreting historic conditions on theTuolumne River (that approach unimpairedconditions), and documenting natural fluvialgeomorphic processes in contemporary alluvialrivers, a set of restoration principles, the“Attributes of Alluvial River Integrity” wasdeveloped to help quantify restoration objectives.The Attributes are:Attribute 1. Spatially complex channel morphology.No single segment of channelbed provides habitatfor all species, but the sum of channel segmentsprovides high-quality habitat for native species. Awide range of structurally complex physicalenvironments supports diverse and productivebiological communities;Attribute 2. Flows and water quality arepredictably variable.Inter-annual and seasonal flow regimes arebroadly predictable, but specific flow magnitudes,timing, durations, and frequencies are unpredictabledue to runoff patterns produced by stormsand droughts. Seasonal water quality characteristics,especially water temperature, turbidity, andsuspended sediment concentration, are similar toregional unregulated rivers and fluctuate seasonally.This temporal “predictable unpredictability”is a foundation of river ecosystem integrity;Attribute 3. Frequently mobilized channelbedsurface.In gravel-bedded reaches, channelbed frameworkparticles of coarse alluvial surfaces are mobilizedby the bankfull discharge, which on averageoccurs every 1-2 years. In sand-bedded reaches,bed particles are in transport much of the year,creating migrating channel-bed “dunes” andshifting sand bars.Attribute 4. Periodic channelbed scour and fill.Alternate bars are scoured deeper than theircoarse surface layers by floods exceeding 3- to 5-year annual maximum flood recurrences. Thisscour is typically accompanied by re-deposition,such that net change in channelbed topographyfollowing a scouring flood usually is minimal. Ingravel-bedded reaches, scour was most likelycommon in reaches where high flows wereconfined by valley walls;EXECUTIVE SUMMARYxix

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOREXECUTIVE SUMMARYAttribute 5. Balanced fine and coarse sedimentbudgets.River reaches export fine and coarse sediment atrates approximately equal to sediment inputs. Theamount and mode of sediment storage within agiven river reach fluctuates, but sustains channelmorphology in dynamic quasi-equilibrium whenaveraged over many years. A balanced coarsesediment budget implies bedload continuity: mostparticle sizes of the channelbed must be transportedthrough the river reach;Attribute 6. Periodic channel migrationand/or avulsion.The channel migrates at variable rates andestablishes meander wavelengths consistent withregional rivers with similar flow regimes, valleyslopes, confinement, sediment supply, andsediment caliber. In gravel-bedded reaches,channel relocation can also occur by avulsion,where the channel moves from one location toanother, leaving much of the abandoned channelmorphology intact. In sand-bedded reaches,meanders decrease their radius of curvature overtime, and are eventually bisected, leavingoxbows;Attribute 7. A functional floodplain.On average, floodplains are inundated onceannually by high flows equaling or exceedingbankfull stage. Lower terraces are inundated byless frequent floods, with their expected inundationfrequencies dependent on norms exhibited bysimilar, but unregulated river channels. Thesefloods also deposit finer sediment onto thefloodplain and low terraces;Attribute 8. Infrequent channel resettingfloods.Single large floods (e.g., exceeding 10-yr to 20-yrrecurrences) cause channel avulsions, rejuvenatemature riparian stands to early-successionalstages, form and maintain side channels, andcreate off-channel wetlands (e.g., oxbows).Resetting floods are as critical for creating andmaintaining channel complexity as lessermagnitude floods, but occur less frequently;Attribute 9. Self-sustaining diverse riparian plantcommunities.Based on species life history strategies andinundation patterns, initiation and mortality ofnatural woody riparian plants culminate in earlyandlate-successional stand structures andspecies diversities (canopy and understory)characteristic of self-sustaining riparian communitiescommon to regional unregulated rivercorridors;Attribute 10. Naturally-fluctuatinggroundwater table.Groundwater tables within the floodway arehydrologically connected to the river, andfluctuate on an inter-annual and seasonal basiswith river flows. Groundwater and soil moistureon floodplains, terraces, sloughs, and adjacentwetlands are supported by this hydrologicconnectivity.Supplemental InvestigationsThe Restoration Plan provides analyses ofhistorical and contemporary hydrologic, fluvialgeomorphic, riparian, and chinook salmon habitatconditions to the extent that data were available,incorporating relevant information from publishedliterature and professional experience, andfrom the extensive investigations on salmonecology conducted on the Tuolumne River by theTID/MID, USFWS and CDFG. In addition, theRestoration Plan conducted geomorphic andriparian investigations to determine the extent towhich specific Attributes are attained underregulated sediment and streamflow conditions,and to provide baseline data for evaluatingrestoration options. These evaluations included:• Fluvial geomorphic processes: identify reachesthat impede gravel transport, estimatestreamflow thresholds for gravel transport,measure gravel and sand transport ratesdownstream of La Grange Dam, identify finesediment sources, evaluate the M.J. Ruddy 4-Pumps restoration project, and develop channeldesign objectives based on these evaluations;• High flow releases: Consider ways to re-operateflood control releases to achieve fluvial geomorphicthresholds;xx

EXECUTIVE SUMMARY• Aggregate source inventory: Locate andestimate volumes of aggregate sources alongthe Tuolumne and Merced Rivers that areavailable for restoration purposes;• Riparian vegetation evaluation: conduct acomprehensive, corridor-wide riparian inventory,and develop relationships between fluvialgeomorphic processes and natural riparianregeneration.Goals and Objectives of the Restoration PlanThe heart of the Restoration Plan is provided in aset of principles and actions that, if fully implemented,would help re-establish fluvial geomorphicfunctions, processes, and characteristics,within contemporary regulated flow and sedimentconditions. This strategy will most effectivelypromote the recovery and maintenance of aresilient, naturally producing chinook salmonpopulation and the river’s natural animal andplant communities. These principles and actionsare contained in five progressively more detailedsections in Chapter 4, including: (1) a statementof restoration goals and objectives, includingexisting programs (CDFG, USFWS/AFRP, andCALFED), the FERC Settlement Agreementgoals and objectives, and river-wide restorationgoals developed in this Plan, (2) formulation ofappropriate restoration strategies for the gravelbeddedand sand-bedded zones, and for each ofthe seven reaches of the Tuolumne River, (3)specific restoration and preservation approachesthat are appropriate for different restorationneeds, (4) identification of restoration sites alongthe entire 52 mile corridor, contained in acomprehensive list with specific information foreach site, and finally (5) a set of restorationconceptual designs for 14 high priority projects,which should be among the first group of projectsto be implemented.The long-term goals for restoring the TuolumneRiver, developed in this Restoration Plan, are:• A continuous river floodway from La GrangeDam to the confluence with the San JoaquinRiver with capacity that safely conveys at least15,000 cfs above Dry Creek and 20,000 cfsbelow Dry Creek;• A continuous riparian corridor from La GrangeDam to the San Joaquin River confluence, witha width exceeding 500 ft minimum in thegravel-bedded zone to a width up to 2,000 ftnear the San Joaquin River;• A dynamic alluvial channel, maintained by floodhydrographs of variable magnitude and frequencyadequate to periodically initiate fluvialgeomorphic processes (e.g., mobilize channelbedsurface, scour and replenish gravel bars,inundate floodplains, and promote channelmigration);• Variable streamflows, such as during chinookspawning, rearing and emigration, to benefitsalmon and other aquatic resources.• A secure gravel supply to replace graveltransported by the high flow regime, thusmaintaining the quantity and quality of alluvialdeposits that provide chinook salmon habitat;• Bedload transport continuity throughout allreaches;• Chinook salmon habitat created and maintainedby natural processes, sustaining a resilient,naturally reproducing chinook salmon population;• Self-sustaining, dynamic, native woody riparianvegetation;• Continual revision of the adaptive managementprogram, addressing areas of scientific uncertaintythat will improve our understanding ofriver ecosystem processes and refine futurerestoration and management;• Public awareness and involvement in theTuolumne River restoration effort;• A clean river. Our perception of a river’sintrinsic value is largely based on visualaesthetics. To most people, a clean river isworth caring for, and the public will be moreconscious of keeping it clean.Restoration Approaches and Site IdentificationA fundamental component of the Restoration Planwas to identify and describe potential restorationsites along the lower Tuolumne River corridor.Restoration sites were identified through severalmethods, and assessed during numerous fieldvisits. Vital statistics for each site (including rivermile and reach location, area, project type,property ownership, a project description andprescription) were tabulated and entered into theTuolumne River GIS. This comprehensive effortresulted in 184 potential restoration sites. Goingfrom 184 potential restoration sites to on-thegroundimplementation requires a technically validprioritization procedure, extensive landownerparticipation and support, planning, projectEXECUTIVE SUMMARYxxi

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOREXECUTIVE SUMMARYmanagement, and engineering. The TuolunmeRiver Technical Advisory Committee, districts,regulatory agencies, and consultants provide thisinfrastructure.Adaptive Management and ImplementationEcosystem restoration is by necessity experimental,driven by hypotheses advanced by greaterunderstanding of physical processes and interactivebiotic responses. The Restoration Planrecognizes recovery will depend on adaptivemanagement by the Tuolumne River TechnicalAdvisory Committee (TRTAC) to regularlyevaluate project successes and failures, and thenrefocus objectives if needed. The recommendedadaptive management approach is similar to thestrategy outlined as Adaptive EnvironmentalAssessment and Management (AEAM) (Holling1978), which stresses explicit integration ofscientific, economic and social concerns intoefforts addressing resource problems. Objectivesfor adaptive management should include: (1) definepolicy and management objectives for satisfyingthe restoration principles, (2) document the statusand trends in chinook salmon populationdynamics, continuing with the outlined FERCmandated monitoring plan, and (3) intertwine thefirst two objectives, is to define restorationendpoints.These are ambitious goals for any program, butmuch more so for a program attempting largescaleecological restoration of a river the size ofthe Tuolumne River. We must acknowledge theinherent uncertainty of our actions, weighpossible outcomes with considerable caution, thenproceed with the best techniques available. Thereis no solution to this scientific uncertainty.Adding the social, political, and economicuncertainties makes river restoration moredaunting. But this daunting task does not justifyinaction, and the stakeholders involved in theimplementation of this Restoration Plan must bewilling to accept success with periodic setbacks,substantial amounts of time and money, and therisks involved in decision making.Copies of this report, or a 16 page Summary of the Habitat Restoration Plan for the Lower Tuolumne RiverCorridor may be obtained from:The Turlock Irrigation District333 E. Canal DriveTurlock, CA 95381(209) 883-8300xxii

INTRODUCTION1 INTRODUCTION1.1 GEOGRAPHIC SETTINGThe Tuolumne River is located in the CentralValley of California and is the largest tributary ofthe San JoaquinRiver (Figure 1-1).The Tuolumne Riveroriginates near11,000 ft elevationin the SierraNevada range,and flowssouthwesterlybetween theMerced Riverwatershed to thesouth and theStanislaus Riverwatershed to thenorth, draining 1,900square miles of westslopingmountains. Itjoins the San JoaquinRiver at RM 83.0,approximately ten mileswest of the City of Modesto.Runoff from the TuolumneRiver is typified by late springand early summer snowmelt,typical of other rivers originatingin the Sierra Nevada mountains.Annual water yield from theTuolumne River averaged 1,906,000acre-feet (af) from 1896 to 1999.The Lower Tuolumne River, extending from LaGrange Dam at RM 52.2 to the confluence withthe San Joaquin River at RM 0.0, is the riversegment under study in this document (Figure 1-2). The Lower Tuolumne River (henceforthreferred to simply as the Tuolumne River) isprimarily alluvial, with bed and banks composedof sand, gravel, and cobble, with occasionalexposed bedrock in areas where the steep bluffs ofthe valley wall confine the channel. Along itslongitudinal gradient the river traverses a varietyof geomorphic and land use zones, includinggravel and sand-bedded zones, the cities of LaGrange, Waterford, and Modesto, agriculturalareas (row crops and orchards), cattle grazing,and aggregate mining. A narrow band of riparianhardwood forest borders the river channel. LaGrange Dam is the lowest in elevation of severaldams constructed in the watershed. La GrangeDam is located at the base of the Sierra Nevadafoothills, downstream of most major tributaries.Dry Creek, which enters the Tuolumne River inModesto (RM 16.2), is the largest tributary in thelower river. During large winter rainstorms, DryCreek contributes significant but short durationflood flows to the Tuolumne River. Agriculturalreturn flows and canal spillways also contributeminor flow volumes to the river below La GrangeDam. None of the tributaries downstream of LaGrange Dam contribute significant volumes ofcoarse sediments; however, fine sediment contributionis often substantial during moderate andlarge rainfall runoff events.The Tuolumne River has been impacted byhuman activities, including gold dredging,aggregate mining, agricultural and urbandevelopment, and water storage anddiversion. These activities have decreasedthe floodway capacity, reduced oreliminated the low-flow andbankfull channel confinement,degraded the channel morphology,decreased the frequencyof large floods, decreasedthe variability of interannualand seasonalflows, eliminatedcoarse sedimentsupply, createdlarge in-channeland off-channelaggregate extractionpits, reducedriparian vegetationcoverage andstructural diversity,Figure 1-1. Location of the and increased theTuolumne River, Stanislaus distribution andCounty, California.abundance of nonnativeplant, fish, and wildlife species. Thecumulative effects of these changes has reducedthe quantity and quality of instream habitat forthe fall-run chinook salmon (Oncorhynchustshawytscha), made the salmon populationunstable, limited native riparian regeneration, anddiminished the quantity and quality of terrestrialhabitat. In short, the Tuolumne River corridorecosystem is heavily degraded.CHAPTER 11

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 1Figure 1-2. Tuolumne River downstream of the New Don Pedro Project (NDPP), showing urban areas, tributaries, TID/MID regulation facilities, and major roads.1.2 PRECURSORS TO THISRESTORATION PLANThe Tuolumne River has an extensive history offlow regulation and diversion by the TurlockIrrigation District (TID), Modesto IrrigationDistrict (MID), and the City and County of SanFrancisco (CCSF). The City and County of SanFrancisco manages three reservoirs on the upperTuolumne River (Figure 1-3): Hetch-HetchyReservoir on the upper mainstem Tuolumne River(363,000 af), Lake Eleanor on Eleanor Creek (27,000af), and Lake Lloyd on Cherry Creek (268,000 af)for a combined storage capacity of 658,000 af.The Districts (TID/MID) have jointly operatedwater storage and diversion facilities on theTuolumne River near La Grange for over acentury (Johnston 1997). The first major facility,La Grange Dam, was constructed in 1893 andcontinues to serve as the diversion point for theTID and MID main canals. Additional storageneeds on the river resulted in construction of theoriginal Don Pedro Dam in 1923 (with a storagecapacity of 290,000 af), which was replaced bythe New Don Pedro Dam in 1970. The New DonPedro Project (NDPP) is the largest mainstemstorage facility on the Tuolumne River, with acapacity of 2,030,000 acre-feet. Construction ofFigure 1-3. Major streamflow diversion structures and volumes of water diverted from the Tuolumne River basin (watervolumes are 1984-1998 averages).2

INTRODUCTIONCHAPTER 1NDPP was a joint project of TID, MID, CCSF, andthe Army Corp or Engineers (ACOE). The NewDon Pedro Project diverts an average of nearly900,000 af annually, delivering 575,000 af to TIDcustomers, and 310,000 af to MID customers. Anadditional 230,000 af are diverted from the upperwatershed by CCSF for delivery of municipal watersupplies to the San Francisco Bay metropolitanarea (Figure 1-3).The Federal Power Commission (later to becomethe Federal Energy Regulatory Commission[FERC]) issued a license for the NDPP in 1964,which required the Districts, in cooperation withfederal and state resource agencies, to conductstudies on the Tuolumne River “aimed at assuringcontinuation and maintenance of the salmonfishery in the most economical and feasiblemanner” (Article 39). Studies were conductedcooperatively by the Districts, U.S. Fish andWildlife Service (USFWS), and CaliforniaDepartment of Fish and Game (CDFG) under a1971 study plan, which was subsequentlyupdated in 1986. These studies described thesalmon ecology and provided managementrecommendations for the Tuolumne River, andare summarized in a series of reports by EAEngineering, Science and Technology (EA 1992;1997). The Tuolumne River is one of the mostintensively studied and documented tributarystreams in the Sacramento/San Joaquin Riversystem, and this Restoration Plan attempts tointegrate this knowledge with additional analysesand recommendations needed to improve andsustain the salmon population.In 1992, FERC began proceedings in response toArticle 37 of the original NDPP license, whichrequired re-evaluation of minimum flow releasesafter the first 20 years of project operation. Theresulting 1995 FERC Settlement Agreement(Settlement Agreement or FSA) was entered intoamong stakeholder groups including the FERC(Commission), TID and MID (Districts), CADepartment of Fish and Game (CDFG), US Fishand Wildlife Service (USFWS), the City andCounty of San Francisco (CCSF), San FranciscoBay Area Water Users Association (BAWUA),Friends of the Tuolumne (FOTT), the TuolumneRiver Preservation Trust (TRPT), TuolumneRiver Expeditions (TRE), and CA Sports FishingProtection Alliance (CSFPA). The Commissionadopted a FERC Order in 1996 amending the FERClicense, which subsequently increased minimum3

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 1Figure 1-4. Timeline of specific actions required by the FERC Settlement Agreement.instream flow requirements. The FERC Orderrequired additional reporting on non-flow mitigativemeasures and an expanded monitoringprogram.The 1995 Settlement Agreement outlined ageneral strategy for restoring the declining fallrunchinook salmon fishery (Sections 8-13 of theFSA), and appointed the Tuolumne River TechnicalAdvisory Committee (TRTAC) to overseeimplementation of the restoration measures. TheTRTAC then chose to prepare a restoration plan toguide planning and implementation of a comprehensiverecovery program. The TRTAC in March1996 approved a pilot geomorphic and salmonidhabitat restoration assessment of the lowerTuolumne River downstream of La Grange Dam(McBain and Trush 1996). This pilot assessmentled to full-scale development of an integrated,long-term restoration plan for the lowerTuolumne River mainstem. This restoration planwould more thoroughly evaluate general biologicaland geomorphic watershed processes affectingriver ecosystem health and fall-run chinooksalmon habitat conditions, gauge the river’srestoration potential within present socioeconomicconstraints, and guide the design andprioritization of river-wide restoration projects.Additional tasks for the restoration plan included:• A review of recent biological studies toevaluate factors potentially limiting chinooksalmon productivity;• Fluvial geomorphic and hydrologic investigationsto document physical processes mostimportant to river ecosystem restoration in theLower Tuolumne River;• Riparian investigations to document historicconditions and contemporary processes thatpromote natural regeneration of riparianvegetation;• Evaluation of coarse and fine sediment budgets,including an assessment of tributary andagricultural runoff inputs of fine sediment (siltand sand), and identification of reachespotentially restricting coarse sediment(bedload) transport, and strategies for restoringcoarse sediment equilibrium;• Inventory of all aggregate sources potentiallyavailable for use in future restoration projectson the Tuolumne River, along with evaluationof costs and recommendation of strategies forutilizing materials;• Evaluation of opportunities for re-operation offlood control releases for fluvial geomorphicprocesses.This Habitat Restoration Plan for the LowerTuolumne River Corridor (Restoration Plan) isthe result of efforts by the TRTAC to develop anintegrated, long-term plan, pursuant to thedirection in the FERC Settlement Agreement, thatwill improve naturally occurring salmon populations,improve riparian habitat, and improvephysical processes that create and maintain riverform and function. The timeline for specificactions required by the FERC Settlement Agreement,as well as other programs related toTuolumne River habitat restoration activities areoutlined in Figure 1-4.4

INTRODUCTION1.3 CLARIFICATION OFTERMINOLOGY1.3.1. Restoration versus RehabilitationThe term “restoration” often implies a return to apreferable or pristine condition that existedhistorically. Unfortunately, barring removal of thedams, cessation of agricultural and miningactivities within the valley, elimination of waterdiversion and other large-scale changes, returningto a pre-settlement Tuolumne River corridor isimpossible. “Rehabilitation” more realisticallydescribes our task outlined in this RestorationPlan, which is to improve conditions within theTuolumne River corridor to the fullest extentpossible given fluvial geomorphic, hydrologic,and societal constraints, with the understandingthat a complete return to pre-degraded conditionsand salmon population levels is not feasible.Figure 1-3 illustrates these concepts. We willcontinue, however, to use the more familiar term“restoration” throughout. The reader must keep inmind that what is intended is “rehabilitation” tohelp achieve the goals of the Settlement Agreement.Defining the restoration needs of the TuolumneRiver must be based on a sound foundation ofinformation and understanding that will lead tothe greatest chance for improving the rivercorridor. A restoration plan must also have afoundation in river ecology (Stanford et al. 1996).Figure 1-5. Different states of ecosystem recovery based on changesin ecosystem structure and function (modified from Bradshaw, 1984).Note that restoration is near or at original ecosystem structure andcomplexity. Rehabilitation improves ecosystem structure andcomplexity, but not to original (historical) levels.This Restoration Plan incorporates both foundations.Therefore, while chinook salmon are aprimary target species, the health and integrity ofthe ecosystem are given equal priority.1.3.2. Historical salmonid populationsThe Tuolumne River historically supported at leastthree major runs of anadromous salmonids (seagoingruns): fall-run and spring-run chinooksalmon (Oncorhynchus tshawytscha), andsteelhead trout (Oncorhynchus Mykiss). Theseruns differed in both timing of major life-historystages such as upstream migration, spawning,duration of residence in freshwater, and emigrationto the Pacific Ocean, as well as their adaptationsto instream habitat. The fall-run salmonhistorically spawned during fall and early wintermonths in the mainstem reaches of Central Valleyrivers below the foothills, up to approximately1,000 ft in elevation. In contrast, the spring-runsalmon ascended higher into accessible tributariesabove the foothills, and depended on cold-waterholding habitat during warm summer months,before spawning during fall and early wintermonths (Healey 1991, Yoshiyama et al. 1998).Steelhead trout also ascended higher into CentralValley tributaries to spawn during late-fall andwinter months. Because of these general differencesin life history timing and habitat requirements,each run responded uniquely to major landuse developments that have occurred during thepast century. The spring-run chinookpopulation, believed to have been themost abundant salmon in the SanJoaquin River basin, is now extinct,blocked from its former over-summeringand spawning habitat by dams. Thesteelhead may still persist in relativelysmall numbers, but debate over itshistorical distribution and less emphasisin its commercial value has shiftedthe primary focus away from restoringa viable steelhead run. Only the fall-runchinook salmon run has persisted inappreciable numbers during the lastfew decades, and now retains thedistinct status in the San Joaquin Riverbasin and the Tuolumne River as apotentially viable commercial andrecreational fishery worthy of significantand costly basin-wide restorationefforts.CHAPTER 15

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 1The primary fishery focus of this Restoration Planis therefore the fall-run chinook salmon population,while secondarily acknowledging the historicalabundance and importance of other nativesalmonid species. Henceforth, references tochinook salmon or salmon are specifically to thefall-run population.1.3.3. Ecosystem-based approach torestorationThis Restoration Plan parallels several ongoingrestoration programs targeting California’s inlandand estuarine water resources. The USFWSAnadromous Fish Restoration Program (AFRP)responded to federal legislation (CVPIA 1992)with the explicit goal of doubling naturalproduction of anadromous fish in Central Valleystreams. The CALFED organization is aconsortium of federal and state resource agenciesmandated by the Bay-Delta Accord with broadobjectives of restoring the San Francisco Bay-Delta resources, Sacramento/San Joaquin Rivers,and their tributary streams. The San JoaquinRiver Management Program was developed by theCalifornia Department of Water Resources(DWR) and the US Bureau of Reclamation(USBR) to address problems in the San JoaquinRiver and its tributary streams. The CDFG“Central Valley Salmon and Steelhead Restorationand Enhancement Plan” (CDFG 1990)outlines CDFG’s restoration and enhancementgoals for salmon and steelhead resources of theSacramento and San Joaquin river systems.Finally, the CDFG “Restoring Central ValleyStreams: A Plan For Action” (CDFG 1993) wasdeveloped to assess present conditions and needsof Central Valley anadromous fish habitat andassociated wetlands, then set priorities for takingaction to restore and protect California’s aquaticecosystems.Cumulatively, these diverse interests, plans, andefforts reinforce the need for a comprehensivestrategy, reached by consensus among thestakeholder groups comprising the TRTAC, forrehabilitating the Tuolumne River corridor. Onmany rivers, past management and restorationactivities focused primarily on a single species orcommercially valued species rather thanecological/physical processes, and success hasbeen limited. Management efforts to improvebiodiversity and productivity have also largelyfailed (Stanford et al. 1996). Our approach torehabilitate the Tuolumne River corridor centersupon restoring hydrologic and fluvial geomorphicprocesses that are responsible for creatingand maintaining river form and function. This,in turn, provides the physical habitat needed tosupport native aquatic and terrestrial communities.We hypothesize that restoring the foundationof the Tuolumne River ecosystem (the physicalhabitat) will improve salmon habitat and thus thefall-run salmon population. In this respect, wetherefore consider this approach “ecosystemrestoration”, while acknowledging that thisrestoration approach does not explicitly addressevery aspect of the ecosystem.Thus, the Restoration Plan is based on thehydrologic and fluvial geomorphic processes 1 thatform and maintain habitat conditions, andtherefore control the life histories and distributionof native aquatic and terrestrial communities.Understanding the fundamental ecologicalprocesses helps identify ways in which humanactivities have influenced those processes, andthen understand the collateral responses of the lifehistories of the biota. However, recognizing thatchinook salmon are a commercially and sociallyvalued species suggests that our approach unitethe best features of single-species management(for chinook salmon), ecosystem restoration andmanagement (to include ecological processes andhuman influences), and adaptive management (toaddress uncertainty in management actions). Thiscombined approach offers the opportunity totarget chinook salmon restoration goals of theFSA, CDFG, AFRP, and CALFED, and concurrentlypursue broader objectives of rehabilitatingself-sustaining ecological processes on theTuolumne River.This Restoration Plan thus focuses on large scalephysical processes, past and present land useactivities, and streamflow regulation, in additionto individual species, granting that the primaryfocus on chinook salmon is socially and economicallyimportant. In this strategy, ecologicalprocesses are intended as tools to maintain thosespecies and communities more universally valued(Simberloff 1998). This strategy is consistent withthe focus and direction of the primary principles1Henceforth, the term ‘fluvial geomorphic processes’will be referred to more simply as ‘fluvial processes’.6

INTRODUCTIONarticulated in the Settlement Agreement. Additionally,the needs of individual species are fundamentallylinked to ecosystem processes. Manyphysical elements proposed for rehabilitation arethe same habitat features that potentially limitsalmon production. This combined approachallows flexibility in responding to short-termneeds of salmon production while simultaneouslypromoting a long-term vision for a healthyecological community.As an example, the Restoration Plan provides therationale and guidelines for coarse sedimentmanagement (spawning gravel introduction) toprovide improved salmon spawning conditions(short-term needs), and concurrently recreateconditions which will promote channelbed scourand redeposition, and channel confinement (longtermvision) in presently degraded river reaches.1.4. SCOPE OF THE RESTORATIONPLAN1.4.1. Corridor versus watershedboundariesRestoration plans typically delineate geographiclimits and target specific species and/or specifichabitats. Contemporary watershed analyses usenatural watershed boundaries as the geographiclimits, rather than using arbitrary boundaries suchas county or state lines. These plans also incorporatenumerous species that are found within thewatershed boundaries. This report does notadhere to the format and breadth of a standardwatershed analysis, primarily because the upperTuolumne River watershed above NDPP isecologically and geographically isolated from thelower Tuolumne River corridor. Instead, thisRestoration Plan is limited geographically to the52.2 mile lower Tuolumne River floodway belowNDPP, including the river channel, adjacentfloodplains, and the bluffs which confine theupper reaches. In the lower valley, geographiclimits are less distinct, but the floodway shouldinclude an appropriate corridor width to containlarge floods and mature riparian stands.Though originally conceived as a watershedanalysis, our approach should be considered ariver corridor analysis and restoration plan. Weare not attempting to separate the river from itswatershed; however, often the first hurdle for aproposed restoration project is to limit theproject’s scope to maintain its effectiveness. TheTuolumne River downstream of La Grange Damis both a logical and practical division because theNDPP effectively isolates the upper watershedfrom the lower watershed. An important objectiveis to determine if a successful salmonid habitatand river ecosystem restoration strategy caneffectively occur at the scale of the river corridorbelow the NDPP. If not, how far and how much ofthe surrounding watershed should be included.Acknowledging that the NDPP eliminatessediment supply from the upper watershed, blocksanadromous fish access to the upper watershed,and effectively dictates hydrologic conditionsdownstream, suggests that longitudinal boundariesof this Restoration Plan should extend alongthe Tuolumne River corridor from La GrangeDam (RM 52.2) downstream to the San JoaquinRiver confluence (RM 0.0).Alluvial rivers such as the Tuolumne River aredynamic, and their spatial dimensions varyconsiderably. A river channel cannot function asan ecosystem independent of the floodplains andhistoric terraces that are formed and maintainedby fluvial processes. The Tuolumne River corridormust include a floodway that, in many locations,requires much greater capacity than now existsfor the river to predictably and beneficiallyfunction at high flows. Increasing floodwaycapacity will also improve flood control managementand buffer adjacent lands from the riverchannel. Sequences of historical photos show thatthe corridor width has been progressively reducedby land use. This Restoration Plan must thereforeincorporate strategies for maintaining andincreasing the corridor width, and maintain arestored floodway as a primary component of theecosystem.1.4.2. Focus on natural chinook salmonproductionWithin the framework of this Restoration Plan,the explicit connection of ecosystem rehabilitationefforts to chinook salmon production is a keyfeature. Several programs, including the FSA,AFRP and CALFED expressly mandate restoringand managing for natural chinook production, incontrast to artificial production or supplementationas the primary restoration strategy. TheFERC Settlement Agreement, for example, statesthat the recovery strategy for chinook salmonshould attempt to “increase naturally occurringCHAPTER 17

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 1salmon populations” using measures that include“increased flows, habitat rehabilitation andimprovement, and measures to improve smoltsurvival.” The USFWS AFRP established aproduction target (harvest and escapement) of38,000 fall-run chinook salmon as a multi-yearaverage for the Tuolumne River. The AFRP alsospecifies natural salmon production, defined bythe AFRP as “fish produced to adulthood withoutdirect human intervention in the spawning,rearing, or migration processes”. The goal of thisRestoration Plan in relation to salmon production,therefore, is in accordance with natural productiongoals mandated by the FERC SettlementAgreement and the Anadromous Fish RestorationProgram.1.5. OBJECTIVESObjectives of this Restoration Plan were developedduring an initial scoping document (McBainand Trush 1996), and have been refined since.Objectives include:1. Develop hypotheses to relate historicalfluvial processes, channel morphology, andriparian vegetation to the ecological healthand integrity of the Tuolumne River. Relateattributes of ecosystem integrity to salmonidphysiology and life history strategies, anddevelop restoration goals based on theseinter-relationships.2. Evaluate opportunities for restoring andincreasing intra-annual flow variability, suchas during chinook spawning, rearing andemigration, to benefit salmon and otheraquatic resources.3. Evaluate the coarse sediment budget,identifying sediment supply sources andbedload “traps” that impede coarse sedimentrouting through the river.4. Identify fine sediment sources that negativelyimpact chinook habitat, and develop remedialstrategies.5. Identify opportunities for achieving fluvialgeomorphic thresholds via flow releaseprescriptions for NDPP, coarse sedimentintroduction, and channel reconstruction.6. Inventory and classify existing riparianvegetation to establish baseline conditions,evaluate factors that limit natural riparianvegetation recruitment, and identify potentialriparian restoration sites.7. Identify, prioritize, and develop proposals forchannel reconstruction projects.8. Develop a restoration vision forgeomorphically distinct reaches of theTuolumne River, and river-wide.9. Integrate site specific and river-widemonitoring plans to evaluate future restorationefforts, which can be easily used foradaptive management by the TRTAC.A successfully implemented river corridorrestoration plan must contain the followingcomponents:• A science-based understanding of the rivercorridor and the biological communities withinit;• Identification of opportunities and constraintsto restoration, including water supply, landownership, sediment supply, and developmentalong the river;• A technical stakeholder group to evaluate andimplement restoration activities;• Support of the Restoration Plan by the localcommunity.The first two components are largely in place.The Tuolumne River Technical Advisory Committeehas assumed responsibility for the thirdcomponent, and have conducted quarterlymeetings since 1996. The final important step isto share the Tuolumne River restoration visionwith the local community, solicit input from thecommunity, and maintain their involvement infuture activities. Occasionally restoration projectshave been halted by lack of consensus from even asmall segment of the local community. To avoidthis situation, the TRTAC has begun (and willcontinue) the process of “community outreach”,by hosting public meetings and workshops topresent the Restoration Plan and specificrestoration projects, and encourage continuedcommunity involvement.8

INTRODUCTIONTo present the goals and objectives of thisRestoration Plan, the remainder of the documentis structured in the following way:Chapter 2 describes the historical and contemporaryhydrologic and fluvial processes, the biologicaland physical processes that perpetuate riparianvegetation patterns (i.e., the interaction withhydrologic and fluvial processes), and chinooksalmon adaptations to historical hydrological andphysical habitat conditions, and the potentialconstraints that alterations of those conditionsmay impose on the salmon.Chapter 3 describes the technical fluvial geomorphic,hydrologic, and riparian evaluations thatwere conducted as part of development of theRestoration Plan to supplement the alreadyexisting knowledge of chinook salmon life historyand ecology.Chapter 4 presents the restoration vision, restorationstrategies for specific river reaches and riverwide,and various restoration approaches availablefor carrying out the vision and strategies.This chapter also presents a list of restorationsites, and conceptual designs developed forspecific projects.Chapter 5 concludes with strategies for implementingan adaptive management and monitoringprogram, including both river-wide and restorationproject-specific monitoring protocols.Finally, two appendices contain streamflowhydrographs for the lower Tuolumne River, andriparian vegetation inventory and specie list. ACD Rom is also provided that contains a PDF fileof this report, data collected as part of this report,and riparian inventory maps.CHAPTER 19


LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORYCHAPTER 22. LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORYIn the Central Valley, the fall-run chinook salmon isa high priority species demanding considerableenergy and money to rebuild and maintainhealthy populations. Numerous restoration andmanagement approaches have been applied on theTuolumne River, such as instream flow (IFIM)and temperature studies, microhabitat restoration(e.g., riffle reconstruction), each with varyingdegrees of success (Kondolf, et al. 1996).However, most approaches have not beenintegrative, nor have they attempted toincorporate fluvial and hydrologic processes torestore habitat. Chinook salmon life historyadaptations to natural riverine processes are alsofrequently overlooked in restoration strategies.Recognizing that the different seasonal runs, andperhaps some individual populations of chinooksalmon in the Central Valley evolved in responseto particular environmental conditions, and thathuman activities have radically changed thoseconditions, helps explain how salmon populationshave declined so dramatically. This recognitionalso provides a logical point of departure fordeveloping a restoration strategy.The TRTAC, other funding entities, and regulatoryagencies have the authority and theextraordinary opportunity to dramatically improveconditions in the Tuolumne River. Collateralefforts are underway to address ecological andmanagement problems in the Sacramento - SanJoaquin Bay/Delta system and associated watersheds,with goals to improve ecological conditionsfor priority species such as the fall-run chinooksalmon. Ocean harvest regulations have alsobecome much more restrictive in response todeclining salmon populations and increasingpublic pressure. These efforts clearly reflectchanging societal values toward maintainingbiological diversity in the face of increasingdevelopment and use of natural resources. Aprimary objective of the restoration strategyshould be to restore ecological health to theTuolumne River so that it is not the factor limitingnatural salmon production.This chapter examines information on salmonecology and management derived from previousstudies, and describes contemporary knowledge offluvial (and riparian) processes that create andmaintain river ecosystem integrity. Our goal is tointegrate historical and contemporary fluvialgeomorphic and ecological information withmanagement objectives, acknowledging societal11

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 2constraints, to provide a technical foundation andplanning strategy for restoring the TuolumneRiver corridor.Integration first requires a demonstrated understandingof the physical processes that underpinecological integrity and provide salmon habitat.We describe how salmon adapted to historicalhydrologic and fluvial processes prior to largescale human impact to the corridor. “Conditions”refers to the form of the river corridor and thephysical processes that created that form. Ourunderstanding of historical conditions will thensuggest hypotheses of how salmon and otheraquatic and riparian species depended on thoseconditions, which can then be used to supporthypotheses about specific restoration strategies.Defining historical conditions is problematicbecause nearly all quantitative and qualitativedescriptions of the Tuolumne River occurredduring or after major episodes of human impact.Pristine river conditions were never documented.“Historical” therefore refers to the least disturbedconditions for which information exists and inferswhat was natural based on contemporary knowledgeof alluvial river systems. In the followingsections we describe historical and present dayhydrology, fluvial geomorphology, and thebiological resources within the corridor, anddescribe how these components interacted todefine a healthy river ecosystem.2.1. HYDROLOGY2.1.1. The unimpaired flow regimeThe natural or “unimpaired” flow regime historicallyprovided large variation in the magnitude,timing, duration, and frequency of streamflows,both inter-annually and seasonally. Variability instreamflows was essential in sustaining ecosystemintegrity (long-term maintenance of biodiversityand productivity) and resiliency (capacity toendure natural and human disturbances)(Stanford, et al. 1996). Restoring the natural flowvariability of a river is now recognized as afundamentally sound approach to initiating riverecosystem restoration (Poff, et al. 1997). Riverrestoration strategies based on restoring flowvariability have typically been underutilized in thepast, or difficult to implement because of theinherent economic value of water.We begin by presenting key components of thenatural flow regime, using streamflow data prior toinitiation of major storage and diversion systems,in addition to “computed natural flows”, which areapproximated streamflows that would occur in theabsence of storage and diversion. Computednatural flows are calculated from measured inflowsinto Don Pedro Reservoir and diversions fromupper-basin reservoirs. Pre-diversion streamflowdata and computed natural flows are combined togenerate the unimpaired flow record. Long-termdaily streamflow records provide statisticaldocumentation of the annual flow regime. The U.S.Geological Survey (USGS) station at La Grange(#11-289650) best documents flow conditions inthe upper 28-mile gravel-bedded section of theTuolumne River, which contains nearly all thechinook spawning and rearing habitat. Additionally,this gage provides streamflow data used bythe Districts and CCSF to determine annual wateryield. Computed unimpaired streamflows at LaGrange and streamflows measured at La Grangeprovide the following data:• 102 years of unimpaired annual water yieldestimates, in acre-feet (WY1897 to 1998);• 82 years of unimpaired daily averagestreamflows, in cfs (WY1918 to 1999);• 29 years of post-NDPP daily averagestreamflows, in cfs (WY1971 to 1999);• 73 years of pre-NDPP annual instantaneousmaximum flood flow data, in cfs (WY1897 to1970);• 29 years of post-NDPP annual instantaneousmaximum flood flow data, in cfs (WY1971 to1999).Our hydrologic analysis focused on (1) characterizinginter-annual and seasonal variations inmagnitude, timing, duration, and frequency ofdaily average discharge at La Grange, (2) ananalysis of annual water yield, and (3) a floodfrequency analysis. The unimpaired flow regimein the Tuolumne River prior to construction ofNew Don Pedro Dam serves as a baseline forcomparing the post-NDPP regulated flow regime.These analyses are then linked to chinook lifehistory, riparian life history, and potential impactsfrom regulation. Annual hydrographDaily average stream flows were plotted asannual hydrographs at La Grange, for WY1918 to1999 (unimpaired) and WY1971 to 1997 (post-12

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORY16,000Peak discharge = 20,280 cfs14,000Daily Average Discharge (cfs)12,00010,0008,0006,0004,000Fall stormsWinter floodsSnowmelt peakSnowmelt recessionSummer baseflows2,00001-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepWinter baseflowsCHAPTER 2Day of Water YearFigure 2-1. Tuolumne River at La Grange annual hydrograph for WY 1979 (NORMAL water year type) to illustratethe important hydrograph components.NDPP regulation), and are presented in AppendixA. Analyses of streamflow patterns for dailyaverage flow revealed characteristic patternswhich we termed “hydrograph components”.Important hydrograph components for theTuolumne River were fall storm pulses, winterand summer baseflows, winter floods, springsnowmelt floods and snowmelt recession, andtransition periods between components (Figure 2-1). These components were further analyzed todescribe the variability in magnitude, timing,duration, and frequency, and rates of change offlow for five water year types. Additionally, asingle hydrograph for the Tuolumne River wasconstructed by averaging daily streamflows forthe entire period of record. Each hydrographcomponent uniquely influenced the morphologyand function of the channel, as well as riparianvegetation patterns and chinook salmon lifehistory characteristics. This approach wasrecently developed for evaluating the impacts ofregulation on streamflow in the Trinity River,CA (USFWS 1999). Annual water yield and water yeartypesThe annual water yield for unimpaired flows at LaGrange for WY1897 to 1999 was plotted to illustratethe variation in annual yield (Figure 2-2). Averageannual unimpaired water yield for the TuolumneRiver over the 102 years of record is approximately1,900,000 acre-feet (af). Annual yield (Table 2-1)varied widely from a low of 454,000 af (WY1977) to4.6 million af (WY1983). Annual water yields werethen classified into five water year types based onthe frequency distribution of annual yield. Thiswater year classification is not meant to replace theclassification system in the FSA, but is simpler andallows a more descriptive presentation of interannualvariability 2 .2The water year classification system used in the SettlementAgreement is based on the 60-20-20 San Joaquin Index, aformula that differentially weights three factors to determine awater year index: (1) the current year’s estimated April-Julyunimpaired runoff (60%), (2) current year’s estimatedunimpaired October-March runoff (20%), and (3) the previousyear’s index (20%). This classification defines ten water yeartypes for the lower Tuolumne River, with unequal occurrenceprobabilities.13

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR5,000,0004,500,000Annual Yield (acre-feet)4,000,0003,500,0003,000,0002,500,0002,000,0001,500,000Average unimpaired inflow:1,900,000 acre-ftCHAPTER 21,000,000500,000018971901190519091913191719211925192919331937194119451949195319571961196519691973197719811985198919931997Water YearFigure 2-2 Annual unimpaired water yield of the Tuolumne River at La Grange, from WY 1897 to 1999.The water year classification used in the RestorationPlan was developed by plotting WY1918 toWY1999 annual water yields as an exceedenceprobability (WY1897 to WY1917 were excludedbecause the reconstructed data were less reliable).The distribution was then divided symmetricallyinto five equally weighted classes separated byannual exceedence probabilities (p) of 0.80, 0.60,0.40, and 0.20 (Figure 2-3) and named “ExtremelyWet”, “Wet”, “Normal”, “Dry”, and“Critically Dry”. This classification systemaddresses the range of variability in the annualwater yield and provides an equal probability foreach class that a given water year will fall intothat category (equally distributed around themean), which in turn allows simpler interpretationof comparisons between water year types.Differences among and within water year classeshave meaningful geomorphic and biologicalconsequences, and will be discussed later in thischapter.Annual hydrographs grouped into the five wateryear classes were then averaged to produce asingle average hydrograph. Average water yearhydrographs illustrate differences between wateryear classes, but mask natural flow variabilitywithin each class. To highlight the annual flowvariability, we overlaid the water year averagehydrographs with a single unimpaired annualhydrograph from a representative water year(Figures 2-4 to 2-8). We also included the FERCminimum baseflows. Water years 1967, 1940,1946, 1985, and 1987 were selected as representativeyears for Extremely Wet, Wet, Normal, Dryand Critically Dry years, respectively. Water yearclass designations are also indicated on theannual hydrographs plotted for each water year(Appendix A). Hydrograph componentsUnimpaired hydrograph components and theassociated variability in magnitude, timing,duration, and frequency were analyzed for eachwater year class by plotting and inspecting annualhydrographs to provide a mean or median value,peak value, and/or minima and maxima representativeof each water year class (Table 2-2).Important hydrograph components are:14

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORY• Fall baseflows. Occurring between October 1and December 20, these were relatively low flowspunctuated by short duration, small magnitudefall floods. Fall baseflows were the unimpairedflows to which adult chinook salmon wereadapted during the spawning phase of their lifehistory. Average fall baseflows ranged from 300cfs to 550 cfs during Critically Dry and ExtremelyWet water years, respectively, and frequentlyexceeded 1,000 cfs during wetter fall seasons;• Fall floods. Occurring between October 1 andDecember 20, these floods were generally ofsmaller magnitude than winter storms. Medianpeaks ranged from 1,400 cfs to 6,300 cfs forCritically Dry and Wet years, respectively, butexceeded 20,000 cfs seven times duringunimpaired conditions, all during ExtremelyWet and Wet water years;• Winter baseflow. Occurring between December21 and March 20, winter baseflows were lowflows between individual storm events. Winterbaseflows were maintained by the recedinglimbs of storm hydrographs and shallowgroundwater discharge, and generally increasedin magnitude and duration throughout the wintermonths as soils and groundwater tables rose.Flow conditions during winter months werehighly variable, so determining baseflow wasdifficult. Wetter years generally exhibited higherwinter baseflows. Extremely Wet years hadbaseflows ranging from 1,300 cfs to 4,400 cfs,averaging 2,800 cfs. Critically Dry years rangedfrom 300 cfs to 1,200 cfs, averaging 780 cfs;• Winter floods. Typically occurring between mid-December and late-March, winter floods weregenerated by rainfall or rain-on-snow stormevents. Larger magnitude, short duration floodscaused by rainfall and rain-on-snow stormevents typically peaked in late Decemberthrough January, with moderate magnitudeevents extending through March. Winter floodswere described two ways: the standard floodfrequency analysis of instantaneous peak floods(USGS 1982), and peak daily average floods forCHAPTER 25,000,0004,000,000Extremely WetAnnual Runoff (acre-ft)3,000,0002,000,0001,000,000WetNormalDryCritically Dry00% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%Exceedence Probability (P)Figure 2-3. Cumulative plot of ranked annual water yields for the Tuolumne River at La Grange, showing exceedenceprobabilities of annual yield and water year classification scheme.15

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORTable 2-1. Tuolumne River at La Grange annual water yield and water yield classification for unimpaired and post-NDPP regulated conditions. The water year classification is based on unimpaired water yield.CHAPTER 2Water YearUnimpaired wateryield (acre-ft)Post-NDPP wateryield (acre-ft)Water year classification(based on unimpaired water yield)Rank(1-82)ExceedenceProbability1897 2,408,626 N/A NOT USED1898 904,929 N/A NOT USED1899 1,405,080 N/A NOT USED1900 1,709,988 N/A NOT USED1901 2,868,440 N/A NOT USED1902 1,478,285 N/A NOT USED1903 1,732,731 N/A NOT USED1904 2,186,807 N/A NOT USED1905 1,394,306 N/A NOT USED1906 3,309,416 N/A NOT USED1907 3,402,943 N/A NOT USED1908 641,423 N/A NOT USED1909 2,253,531 N/A NOT USED1910 1,784,531 N/A NOT USED1911 2,895,247 N/A NOT USED1912 1,049,518 N/A NOT USED1913 1,081,250 N/A NOT USED1914 2,624,557 N/A NOT USED1915 2,044,411 N/A NOT USED1916 2,488,186 N/A NOT USED1917 2,226,657 N/A NOT USED1918 1,456,903 N/A Normal 47 59%1919 1,337,742 N/A Dry 53 66%1920 1,340,043 N/A Dry 52 65%1921 2,026,884 N/A Normal 36 45%1922 2,447,486 N/A Wet 21 26%1923 1,819,087 N/A Normal 41 51%1924 570,826 N/A Critically Dry 81 101%1925 1,940,010 N/A Normal 39 49%1926 1,138,400 N/A Dry 62 78%1927 2,069,819 N/A Wet 32 40%1928 1,562,925 N/A Normal 44 55%1929 1,004,076 N/A Critically Dry 71 89%1930 1,166,851 N/A Dry 59 74%1931 627,292 N/A Critically Dry 80 100%1932 2,128,335 N/A Wet 28 35%1933 1,120,610 N/A Dry 66 83%1934 843,120 N/A Critically Dry 76 95%1935 2,102,592 N/A Wet 30 38%1936 2,152,228 N/A Wet 27 34%1937 2,022,282 N/A Normal 37 46%1938 3,429,698 N/A Extremely Wet 5 6%1939 995,539 N/A Critically Dry 72 90%1940 2,345,490 N/A Wet 25 31%1941 2,501,575 N/A Wet 19 24%1942 2,363,833 N/A Wet 23 29%1943 2,381,340 N/A Wet 22 28%1944 1,297,111 N/A Dry 55 69%1945 2,095,788 N/A Wet 31 39%1946 1,887,704 N/A Normal 40 50%1947 1,098,414 N/A Critically Dry 67 84%1948 1,412,392 N/A Normal 49 61%1949 1,256,930 N/A Dry 57 71%1950 1,557,473 N/A Normal 45 56%16

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORYTable 2-1 cont.Water YearUnimpaired wateryield (acre-ft)Post-NDPP wateryield (acre-ft)Water year classification(based on unimpaired water yield)Rank(1-82)ExceedenceProbability1951 2,485,956 N/A Wet 20 25%1952 2,975,644 N/A Extremely Wet 12 15%1953 1,533,804 N/A Normal 46 58%1954 1,441,268 N/A Normal 48 60%1955 1,139,613 N/A Dry 61 76%1956 3,152,732 N/A Extremely Wet 8 10%1957 1,397,742 N/A Normal 50 63%1958 2,643,558 N/A Extremely Wet 16 20%1959 1,008,562 N/A Critically Dry 69 86%1960 1,067,594 N/A Critically Dry 68 85%1961 745,506 N/A Critically Dry 78 98%1962 1,776,171 N/A Normal 42 53%1963 2,045,209 N/A Normal 35 44%1964 1,131,801 N/A Dry 64 80%1965 2,744,866 N/A Extremely Wet 15 19%1966 1,313,905 N/A Dry 54 68%1967 3,110,883 N/A Extremely Wet 9 11%1968 1,005,905 N/A Critically Dry 70 88%1969 3,858,598 N/A Extremely Wet 3 4%1970 2,903,749 N/A Extremely Wet 14 18%1971 1,696,685 345,889 Normal 43 54%1972 1,228,740 163,878 Dry 58 73%1973 2,066,837 165,014 Wet 33 41%1974 2,306,285 375,652 Wet 26 33%1975 2,066,348 561,473 Wet 34 43%1976 699,777 360,014 Critically Dry 79 99%1977 454,334 67,115 Critically Dry 82 103%1978 2,932,759 292,052 Extremely Wet 13 16%1979 1,957,501 657,186 Normal 38 48%1980 3,040,767 1,493,029 Extremely Wet 10 13%1981 1,130,446 441,488 Dry 65 81%1982 3,810,491 1,718,285 Extremely Wet 4 5%1983 4,639,714 3,464,878 Extremely Wet 1 1%1984 2,544,881 1,376,458 Wet 18 23%1985 1,281,836 376,094 Dry 56 70%1986 3,028,685 1,133,989 Extremely Wet 11 14%1987 750,286 283,365 Critically Dry 77 96%1988 843,629 77,660 Critically Dry 75 94%1989 1,362,947 61,029 Dry 51 64%1990 894,134 84,964 Critically Dry 73 91%1991 1,160,524 83,115 Dry 60 75%1992 870,146 80,561 Critically Dry 74 93%1993 2,581,784 240,952 Extremely Wet 17 21%1994 1,136,409 187,313 Dry 63 79%1995 3,939,017 2,184,597 Extremely Wet 2 3%1996 2,348,979 1,183,331 Wet 24 30%1997 3,245,211 1,958,532 Extremely Wet 7 9%1998 3,348,765 1,998,252 Extremely Wet 6 7%1999 2,127,404 973,206 Wet 29 35%Average annualyield 1,906,505 772,047CHAPTER 217

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR30,000WY 1967; annual water yield = 3,110,883 afAverage Discharge (cfs)25,00020,00015,00010,000Average unimpaired flow (EXTREMELY WETwater years 1918-1997); average water yield=3,252,900 afHypothetical FERC Settlement AgreementMinimum Flows- "Median Wet/Maximum"CHAPTER 25,00001-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDay of Water YearFigure 2-4. Average and representative (WY 1967) EXTREMELY WET water year annual hydrographs for theTuolumne River at La Grange.Average Discharge (cfs)30,00025,00020,00015,00010,000WY 1940; annual water yield =2,345,490 afAverage unimpaired flow (WET wateryears 1918-1997); average water yield=2,275,500 afHypothetical FERC SettlementAgreement Minimum Flows- "MedianAbove Normal"5,00001-Oct1-Nov1-Dec1-Jan1-Feb1-MarFigure 2-5. Average and representative (WY 1940) WET water year annual hydrographs for the Tuolumne River atLa Grange.1-Apr1-MayDay of Water Year1-Jun1-Jul1-Aug1-Sep18

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORY30,000WY 1946; annual water yield = 1,887,704 afAverage Discharge (cfs)25,00020,00015,00010,000Average unimpaired flow (NORMAL water years1918-1997); average water yield =1,720,900 afHypothetical FERC Settlement AgreementMinimum Flows- "Intermediate: Below Normal"5,00001-Oct1-Nov1-Dec1-Jan1-Feb1-MarFigure 2-6. Average and representative (WY 1946) NORMAL water year annual hydrographs for the Tuolumne Riverat La Grange.1-Apr1-MayDay of Water Year1-Jun1-Jul1-Aug1-SepCHAPTER 230,000WY 1985; annual water yield = 1,281,836 afAverage Discharge (cfs)25,00020,00015,00010,000Average unimpaired flow (DRY water years 1918-1997);average water yield =1,221,500 afHypothetical FERC Settlement Agreement MinimumFlows- "Median Dry"5,00001-Oct1-Nov1-Dec1-Jan1-Feb1-MarFigure 2-7. Average and representative (WY 1985) DRY water year annual hydrographs for the Tuolumne River at LaGrange.1-Apr1-MayDay of Water Year1-Jun1-Jul1-Aug1-Sep19

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR30,000WY 1987; annual water yield = 750,286 af25,000Average unimpaired flow (CRITICALLY DRY wateryears 1918-1997); average water yield =842,500 afAverage Discharge (cfs)20,00015,00010,000Hypothetical FERC Settlement Agreement MinimumFlows- "Critical and Below"CHAPTER 25,00001-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDay of Water YearFigure 2-8. Average and representative (WY 1987) CRITICALLY DRY water year annual hydrographs for theTuolumne River at La Grange.each water year class. Flood frequency curvesfor the La Grange gaging station were based onthe annual maximum series for pre-NDPP andpost-NDPP hydrology, and included raw dataand a log-Pearson Type III distribution fit to logtransformeddata (Figure 2-9). The 1.5- yearrecurrence interval flood for unimpairedconditions was 8,400 cfs; the 5-year flood was approximately 25,000cfs and the 25-year flood was approximately53,000 cfs (Table 2-3). Theflood of record was approximately130,000 cfs, and occurred in 1862 and1997. The annual maximum dailyaverage flow was also analyzed foreach water year class. Magnitude ofthe median peak flood ranged from2,900 cfs to 19,000 cfs for Critically Dryto Wet years, respectively, withmaxima ranging between 50,000 cfsand 60,000 cfs during Wet andExtremely Wet water years. Dry andCritically Dry years had relativelylower daily average flood peaks, but still rangedabove 15,000 cfs for the Dry year maximum flood(Table 2-2);Table 2-3. Tuolumne River at La Grange pre- and post-NDPPannual maximum series flood frequency data.USGS La Grange GagePre-NDPP 1.5-yr flood8,670 cfsPost-NDPP 1.5-yr flood3,020 cfsPercent of pre-NDPP 35%Pre-NDPP 5-yr flood25,230 cfsPost-NDPP 5-yr flood7,569 cfsPercent of pre-NDPP 30%Pre-NDPP 10-yr flood37,574 cfsPost-NDPP 10-yr flood8,429 cfsPercent of pre-NDPP 22%20

Table 2-2. Important components of annual unimpaired hydrographs of daily average flow for the Tuolumne River at La Grange, analyzed for five different water yearclasses. Based on 1918 to 1997 period.21Hydrograph Components Extremely Wet Wet Normal Dry Critica(probability of exceedence) 20% 40% 60% 80% 10(annual water yield, million acre-feet) >2.55 maf 2.05-2.55 maf 1.39-2.05 maf 1.1-1.39 maf

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 2• Snowmelt floods. They were of lower magnitudeand longer duration than winter floods. Prior toregulation and diversion, this component of theannual hydrograph was the largest contributorto the total annual water yield, with largemagnitude and sustained duration floodspeaking from late April to early June, thenreceding in July and August (Figure 2-10). Themean and median peak magnitudes, and therange of snowmelt floods were determined foreach water year class (Table 2-2). The medianpeak floods ranged from 6,000 cfs to 17,000 cfsfor Critically Dry and Extremely Wet years,respectively, but historically ranged as high as52,000 cfs (the computed inflow into New DonPedro Reservoir on 4/11/1982; this flood, arain-on-snow event, was attenuated by NDPPand peaked at 8,150 cfs at La Grange on 4/15/1982). Dry and Critically Dry water years hadmoderate magnitude snowmelt peaks rangingfrom 5,000 cfs to 15,000 cfs;• Snowmelt recession. Connecting the snowmeltpeak to summer baseflows, the snowmeltrecession extended into summer, generallyoccurring earlier in Dry and Critically Dryyears (July), and later in Extremely Wet wateryears (August). Recession rates ranged from780 cfs/day during the steepest portion of therecession to 112 cfs/day towards the end ofrecession during Extremely Wet water yeartypes, and ranged from 400 cfs/day to 95 cfs/day for Normal and Dry water year types(Figures 2-4 to 2-8). The duration and rate ofsnowmelt recession had ecological significanceto numerous biological populations within theTuolumne River corridor;• Summer baseflow. Beginning at the cessation ofthe spring snowmelt hydrograph, summerbaseflows occurred until the first fall stormsincreased streamflows. Summer baseflowsrepresented minimum annual flow conditions,historically averaging from 150 cfs duringCritically Dry water years, to above 600 cfsduring Extremely Wet water years. Duringsome Extremely Wet water years, the summerbaseflow component was obscured within thesnowmelt recession limb and fall floods, andminimum annual flow conditions were unusuallyhigh. Conversely, during drought years thesummer baseflow occasionally dropped below100 cfs.70,00065,00060,00055,00050,000Discharge (cfs)45,00040,00035,00030,00025,00020,00015,00010,0005,000Pre-1970 Raw data (Q1.5=8,400 cfs)Pre-1970 Log-Pearson III fit (Q1.5=8,400 cfs)Post-1970 Raw data (Q1.5=2,700 cfs)Post-1970 Log-Pearson III fit (Q1.5=2,600 cfs)1997 peak, considered an outlier for the post-1970data set00 5 10 15 20 25 30 35 40 45 50Recurrence Interval (years)Figure 2-9. Annual maximum flood frequency curves for unimpaired and post-NDPP periods at La Grange (STN 11-289650, Drainage Area = 1,900 sq. mi.)22

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORY14,00013,00012,00011,00010,0009,000EXTREMELY WETWETNORMALDRYCRITICALLY DRY1971-97 AverageDischarge (cfs)8,0007,0006,0005,0004,0003,0002,0001,00001-May8-May15-May22-May29-May5-Jun12-Jun19-Jun26-Jun3-Jul10-Jul17-Jul24-Jul31-JulCHAPTER 2Day of Water YearFigure 2-10. Tuolumne River at La Grange, unimpaired annual hydrographs during snowmelt recession for eachwater year class, and the 1971-1997 average hydrograph for the impaired post-NDPP period. Flow duration curvesThe daily average flow duration curve illustratesthe relationship between the frequency andmagnitude of streamflows. Flow duration curveswere developed for both the unimpaired periodand the post-NDPP period at the La Grangegaging station (Figure 2-11). Flow durationcurves offer limited description of streamflowbecause they mask inter-annual and seasonalvariability, but are useful in highlighting thechanges to streamflow caused by regulation. Forexample, the 50% exceedence flow for theTuolumne River (i.e., the median annual flow, orthe flow that was exceeded 50% of the days), wasreduced from 1,064 cfs to 224 cfs by NDPPregulation. The mean annual flow for the TuolumneRiver for the unimpaired period of recordwas 2,544 cfs. The post-NDPP mean annual flowwas reduced to 944 cfs, a 60% reduction.2.1.2. Regulated flow regimeDisruption of natural streamflow patterns on theTuolumne River began in the 1850’s with earlygold mining diversion ditches. However largescalediversions began as early as the 1870s withconstruction and diversion at Wheaton Dam(1871) which was replaced by La Grange Dam(1893). These early dams and diversions loweredsummer baseflows, but were too small to significantlyaffect other hydrograph components. Moresubstantial water storage and flood flow modificationsbegan with construction of Don PedroReservoir (290,000 af storage capacity) and HetchHetchy Reservoir (206,000 af storage capacity) inthe 1920’s. The storage capacity of these reservoirswas 26% of the mean annual water yield.CCSF began exports in 1923. Hetch Hetchy Damwas raised in 1937 to increase storage capacity to360,000 af. Lake Lloyd on Cherry Creek addedanother 268,000 af of storage in the basin in1955. The storage capacity of New Don PedroReservoir (2.03 million af) now exceeds the meanannual water yield for the entire Tuolumne Riverbasin (1.906 million af). With the large watershedstorage capacity and minimum instream flowrequirements (1971 to present), the New DonPedro Project severely diminished the magnitude,timing, duration, and frequency of hydrographcomponents in the post-NDPP era.23

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR16,00015,00014,00013,000Unimpaired flow, WY 1918-1997Post-NDPP, regulated flows WY 1971-1997CHAPTER 2Daily Average Discharge (cfs)12,00011,00010,0009,0008,0007,0006,0005,0004,0003,0002,0001,00000.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00Exceedence Probability (P)Figure 2-11. Daily average flow duration curves for unimpaired and post-NDPP periods at La Grange.As a result of streamflow regulation and diversion,the flow regime on the Tuolumne River is vastlydifferent from the unimpaired flow regime presentedabove. Article 37 of the NDPP FERC licenserequires minimum instream flows to protect fisheryresources. In 1971, these instream flows were set at64,000 af during Dry years (FERC designation), and123,000 af in water years in which mean annualreservoir inflow or water yield exceeded 1 million af(67% exceedence, Table 2-4). Streamflows wereaugmented in the 1996 NDPP FERC licenseamendment, resulting in significantly increasedminimum instream flow requirements, rangingfrom 94,000 af in Critical & Below water years(FERC designation), up to 300,000 af in wateryears above 50% exceedence (Table 2-5).Hydrograph components were analyzed for thepost-NDPP hydrologic regime, and compared tothe hydrograph components of the natural flowregime (Figure 2-12). Annual hydrographsAnnual hydrographs for regulated water years1971 to 1999 were prepared using streamflowdata from the La Grange gaging station ( AppendixA). Annual streamflow patterns have changedsignificantly by NDDP regulation, including:• loss of inter-annual and seasonal variability;• disruption and/or complete loss of hydrographcomponents;• reduction in peak flows;• reduction in baseflows.These changes will be elaborated upon in thefollowing sections. Annual water yieldThe average annual water yield below La GrangeDam has been reduced from 1.906 million af to719,000 af, a 62% reduction in average annualyield. The lowest post-NDPP water yield was61,029 af, occurring in 1989. The highest post-NDPP water yield was 3.46 million af, occurringin 1983.24

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORYTable 2-4. Minimum flow releases from NDPP asrequired by Article 37 of the original FERC License(1971 to 1995).PeriodSchedule ANormal Year(unimpairedinflow >1,000,000 af) Hydrograph componentsSchedule BDry Year(unimpairedinflow between750,000 and1,000,000 af)(cfs)Pre-season flushingflow 2,500October 1-15 200 50October 16-31 250 200November 385 200December 1-15 385 200December 16-31 280 135January 280 135February 280 135March 350 200April 100 85May-September 3 3Annual minimumrelease (acre-feet) 123,210 64,040Hydrograph components were not analyzed byspecific water year class in the post-NDPP periodbecause the data set was smaller for regulatedwater years, and regulation eliminated muchvariability between water years. Changes aresummarized below for the effect of streamflowregulation on each hydrograph component. Ingeneral, minimum instream flows were determinedby the 1971 FERC license flow schedule,presented in Table 2-4.• Fall baseflows are now determined by theFERC Settlement Agreement revised minimumflow schedule (Table 2-5), and is the minimumflow component adhered to most becausereservoir storage is typically low following thesummer diversion season (in contrast, winterbaseflows occasionally are augmented by floodcontrol releases). Baseflows are prescribed forthe period Oct 1 to May 31 by the minimumflow schedule, and range between 100 cfs and200 cfs for the drier 50% exceedence water yeartypes, and 300 cfs for wetter 50% exceedenceconditions. The effect of regulation was evidentin all annual hydrographs. Previously variablestreamflows are now held constant to maximize“weighted usable area” for spawning.• Fall floods were eliminated by NDPP regulationin most water years, and were replaced withminimum instream flows ranging from 100 cfs to300 cfs. Small “attraction pulse flows” usuallyless than 2,000 cfs and dependent on water yearclass, were released in wetter water years.• Winter baseflow during the post-NDPP periodhas been reduced, with a median of 1,080 cfs.While this value is higher than the FERCminimum instream flow requirements, it is stillcomparable to a Dry water year in the unimpairedregime. Flow releases higher than FERCrequirements occur during Wet and ExtremelyWet water years when inflow rates and floodcontrol requirements dictate higher streamflowreleases from the NDPP.• Winter floods have been severely diminished byNDPP regulation, with the frequency andmagnitude of winter floods reduced. The 1.5year recurrence flood (“approximate bankfullflow”) was 8,400 cfs unimpaired (Figure 2-9)as compared to 2,600 cfs under post-NDPPconditions. Additionally, ACOE requires thatflood control releases not exceed 9,000 cfs atthe Modesto gage. This flood control limit hasbeen exceeded only three times since NDPPoperation began, in WY1983, WY1995, and theflood of January 1997, which peaked at60,000 cfs. The turbine capacity of theNDPP powerhouse is about 5,500 cfs, sowinter releases are frequently in the range4,500 cfs to 5,500 cfs. Therefore, maximumannual winter floods post-NDPP are typicallyless than 5,500 cfs, with a low of 409 cfs inWY1977.• Snowmelt floods have been eliminated from theannual hydrograph by NDPP operation, andreplaced with Settlement Agreement-mandatedspring pulse flows intended to stimulate smoltemigration. Water volumes available for springpulse flows range from 11,091 af (comparableto 5,600 cfs for one day) to 89,882 af (comparableto 5,040 cfs for 9 days). Daily averageflows for May and June at La Grange werereduced from 7,231 cfs unimpaired to 1,371cfs actual flow (May), and 5,938 cfs unimpairedto 898 cfs actual flow (June). Summerminimum instream flows established by theFERC NDPP license begin June 1.CHAPTER 225

CHAPTER 226Table 2-5. Revised minimum flow releases from NDPP required by FERC License article 37 amendment (1995 to present).Year TypeCritical &BelowMedianCriticalIntermediateC-DMedian DryIntermediateD-BNMedian BelowNormalIntermediateBN-ANMedian AboveNormalIntermediateAN-W% Occurrence 6.4% 8.0% 6.1% 10.8% 9.1% 10.3% 15.5% 5.1% 15.4% 13October 1- 100 cfs 100 cfs 150 cfs 150 cfs 180 cfs 200 cfs 300 cfs 300 cfs 300 cfs 300October 15 2,975 ac-ft 2,975 ac-ft 4,463 ac-ft 4,463 ac-ft 5,355 sc-ft 5,950 ac-ft 8,925 ac-ft 8,926 ac-ft 8,926 ac-ft 8,926AttractionPulse Flownone none none none 1,675 ac-ft 1,736 ac-ft 5,950 ac-ft 5,950 ac-ft 5,950 ac-ft 5,950October 16- 150 cfs 150 cfs 150 cfs 150 cfs 180 cfs 175 cfs 300 cfs 300 cfs 300 cfs 300May 31OutmigrationPuse Flow11,091 ac-ft 20,091 ac-ft 32,619 ac-ft 37,060 ac-ft 35,920 ac-ft 60,027 ac-ft 89,882 ac-ft 89,882 ac-ft 89,882 ac-ft 89,88June 1- 50 cfs 50 cfs 50 cfs 75 cfs 75 cfs 75 cfs 250 cfs 250 cfs 250 cfs 250September 30 12,099 ac-ft 12,099 ac-ft 12,099 ac-ft 18,149 ac-ft 18,149 ac-ft 18,149 ac-ft 60,496 ac-ft 60,496 ac-ft 60,496 ac-ft 60,49Volume (acrefeet)94,000 103,000 117,016 127,507 142,502 165,002 300,923 300,923 300,923 300MediaMaxTUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORY• Snowmelt recession was also altered by NDPPoperation. Spring pulse flows are established forfishery management purposes only, and thereceding limb is often early, short and steep,except in wetter years when flood controlreleases occur.• Summer baseflows have been reduced by NDPPoperation. The median baseflow for August 1through September 30 was 37 cfs for the periodWY1971 to 1997, and was as low as 0 cfsduring several sustained drought periods.Beginning in 1995, summer minimum instreamflows from June 1 through September 30 wereincreased by the FERC NDPP license (Table 2-5), and ranged from 50 cfs and 250 cfs forCritically Dry and Normal-Wet water years,respectively.2.2. FLUVIAL GEOMORPHOLOGY2.2.1. Fluvial geomorphic processesRestoration scientists and resource managers areincreasingly recognizing that integrating fluvialprocesses with the life histories of biologicalresources to rehabilitate riverine ecosystems is afundamentally sound approach to restoring nativefish and wildlife populations (Stanford et al. 1996)(NRC 1996) (Lichatowich 1995) (Hill et al. 1991)(USFWS 1999). This section describes historicalfluvial processes in the Tuolumne River, and howthese processes have changed in response towatershed development and land use.Fluvial geomorphology is the study of landformdevelopment by processes associated with runningwater, and the erosion and transport of sediments.Fluvial processes form and maintain the riverchannel, the river corridor, and the alluvial valley.The primary processes are coarse and finesediment transport, sediment deposition, andchannel migration. The river’s physical form (andtherefore the structural complexity of habitat) isgoverned by the interaction of these fluvialprocesses with streamflow hydrology, geologicalcontrols, riparian influences, and human influences.These interactions are numerous andcomplex. Simplifying fundamental cause andeffect relationships helps illustrate how land usepractices initiate channel responses.CHAPTER 2Streamflow X 1000 (cfs)1098765432WinterBaseflowsWinterFloodSpringSnowmelt1994 Unregulated Streamflows1994 Regulated StreamflowsSummerBaseflows101-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepFigure 2-12. Tuolumne River at La Grange annual hydrograph of unimpaired streamflow and post-NDPP streamflowfor WY 1994 (DRY water year type), showing changes in hydrograph components from unimpaired conditions.27

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORSEDIMENT SIZE FINER STREAM SLOPE STEEPERCHAPTER 2SEDIMENTDEGRADATIONAGGRADATIONWATERFigure 2-13. Conceptual flow-sediment balance necessary for channel equilibrium, and channel response todisequilibrium (from Lane 1955).Lane (1955) provided a simple formula to illustratethe way in which rivers balance slope, sedimentparticle size, sediment transport, and streamflow tomaintain a dynamic equilibrium:Q w* S µ Q s* D 50(2-1)where Q w= stream discharge, S = slope, Q s=sediment discharge , and D 50= median grain size(Figure 2-13).A balance in the sediment transport capacityprovided by the high flow regime with sedimentsupplied from the watershed over time anddistance results in a “dynamic quasi-equilibrium,”in which sediment is mobilized, transported, anddeposited. The channel migrates (dynamic), butthe size and shape of the channel remain similar(equilibrium) (Schumm 1977). While thispresentation of the quasi-dynamic equilibriumconcept of sediment supply and transport isconsiderably simplified, its use as a quantifiableobjective to balance flow and sediment supply is apowerful tool for assessing fluvial processes. Italso helps predict channel responses to alteredflow and sediment regimes.Dams, aggregate extraction, agricultural andurban encroachment, and other land uses havecaused sediment imbalances in the TuolumneRiver channel. For example, reduced magnitude,duration, and frequency of high flows imposed byupstream dams has allowed fine sediment toaccumulate in the river. Elimination of coarsesediment supply below the dams and accumulationof fine sediment from reduced flood flowshave degraded chinook salmon spawning habitat.The impact of these imbalances is also a functionof distance along the Tuolumne River because the28

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORYrelationships between slope, sediment particle size,sediment transport, and streamflow changelongitudinally as the Tuolumne River travels fromheadwaters to the San Joaquin River. Differencesin valley slope, valley confinement, particle size,channel forming discharge, and vegetation createlocal variation in channel morphology. Fluvialprocesses and the resultant channel morphologydepend on these longitudinal differences, andmust be incorporated into restoration planning.2.2.2. Geomorphic reach delineationDownstream of La Grange Dam, the TuolumneRiver can be divided into two distinct geomorphiczones broadly defined by the channel slope andbed material: the sand-bedded zone extends fromRM 0.0 to RM 24.0, and the gravel-bedded zoneextends from RM 24.0 to RM 52.0 (Figure 2-14).The transition from gravel-bedded to sand-beddedzones is a remnant of pre-NDPP processes: wherethe valley widens and slope decreases, the riverwas unable to transport gravel and cobble-sizedparticles. These larger particles deposited inupstream reaches, while sand continued to betransported downstream. During moderate andlarger flows the dominant clast in transport isthus different in each zone. The transition fromgravel-bedded to sand-bedded at approximatelyRM 24 caused a noticeable change in planformmorphology: in the sand-bedded zone sinuosityincreased, amplitude increased, meanders becamemore tortuous, and channel migration was morecontinuous than in the upstream gravel-beddedzone. Channel morphology is characteristically ameandering alternate bar morphology, rather thanthe less sinuous alternate bar morphologyprevalent upstream. These changes also influencedthe composition of woody riparian species.These two geomorphically-based zones weresubdivided into seven reaches based on presentand historical land uses, the extent and influenceof urbanization, valley confinement from naturaland anthropogenic causes, channel substrate andslope, and salmon habitat quality. Differencesbetween these reaches warrant unique restorationvisions and strategies. The major reaches are:REACH 1 (RM 0-10.5): “Lower Sand-beddedReach,” defined by agricultural land use andencroachment (row crops and vineyards), novalley confinement during high flows, low slope(

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORin 1970 removed the extensive dredger tailingsthroughout the reach for use as constructionmaterials for the New Don Pedro Project. Thisactivity and subsequent channel reconstructionresulted in a single-thread meandering low waterchannel with low bankfull confinement. Thequality and availability of spawning habitat inthis reach surpasses that of all other reaches.The slope estimates presented above are generalizedfrom the 1969 USGS Channel CapacityStudy (Figure 2-15) and from 1996 water surfaceprofile measurements during high flows equal to orgreater than 5,300 cfs.The following section discusses historic channelmorphology and fluvial processes on the TuolumneRiver. This discussion differentiates thesand-bedded zone from the gravel-bedded zone;however, because a primary distinction betweenthe seven reaches is the degree of human disturbance,an historical differentiation between theseven reaches is not attempted.SAND-BEDDED ZONE (RM 0.0 to RM 24.0)CHAPTER 2REACH 1 (RM 0.0-10.5)Lower Sand-bedded Reach• Sand bed and banks• Longitudinal slope less than.0003• No valley confinement bybluffs• River corridor confined byagricultural encroachment• Land use predominantlyagricultire (row crops andsome grazing)REACH 2 (RM 10.5-19.3)Urban Sand-bedded Reach• Sand bed and banks• Longitudinal slope less than.0003• Moderate valley confinementwithin bluffs• River channel confined byurban and agriculturalencroachment• Land use predominately urbanwith some agriculture (rowcrops)REACH 3(RM 19.3-24.0)Upper Sand-beddedReach• Sand bed andbanks• Longitudinal slopeless than .0003• Little valleyconfinementwithin bluffs• River corridorconfined byagriculturalencroachment• Land use predominatelyagriculture(row crops) withsome ruralencroachmentREACH 4continuedFigure 2-14. Tuolumne River geomorphic reach delineation.30

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORY2.2.3. Channel morphology (crosssection and planform)Prior to flow and sediment regulation, the TuolumneRiver downstream of La Grange behavedalluvially; the channelbed and banks were composedof alluvium (gravel, cobble, boulders), andthe flow regime and sediment supply were adequateto form and maintain the bed and bankmorphology. Variability in hydrologic and geologicalcontrols (e.g., valley width, location andelevation of underlying bedrock) created variableand complex local channel morphologies. Asdescribed in the hydrology section, streamflowswithin a given year and between years varied fromas low as 100 cfs in summer months to peak winterfloods exceeding 100,000 cfs. The valley wallsconfined the river corridor to as narrow as 500 ftnear Waterford (RM 32.0), whereas reachesdownstream of Modesto were virtually unconfined.Bedrock grade control upstream of Modestoalso varied, with exposed bedrock formations nearthe water surface in some locations, and over 50feet below the riverbed in other locations. TheseGRAVEL-BEDDED ZONE (RM 24.0-52.1)CHAPTER 2REACH 7(RM 46.6-52.1)Dominant SpawningReach• Gravel bed andbanks• Longitudinal slopebetween .0010 and.0015• Little valleyconfinement withinbluffs• River corridorconfined byriparian encroachment• Land use predominatelyagriculture(livestock grazing)• Remnant dredgertailings fromhistoric goldmining, most ofwhich was removedfor New Don PedroProject constructionREACH 4 (RM 24.0-34.2)In-Channel Gravel MiningReach• Gravel bed and banks• Longitudinal slope between.0003 and .0015• Little valley confinementwithin bluffs• River corridor confined byagricultural encroachment• Land use predominatelyoff-channel aggregateextraction and agriculture(orchards)• Extensive history of inchannelaggregate extractionREACH 5 (RM 34.2-40.3)Gravel Mining Reach• Gravel bed and banks• Longitudinal slopebetween .0010 and .0015• Moderate to little valleyconfinement within bluffs• River corridor confinedby agricultural encroachmentand dikes separatingriver from off-channelmining pits• Land use predominatelyoff-channel aggregateextraction and agriculture(orchards and row crops)REACH 6 (RM 40.3-46.6)Dredger Tailing Reach• Gravel bed and banks• Longitudinal slopebetween .0010 and.0015• Little valley confinementwithin bluffs• River corridor confinedby riparian encroachment• Land use predominatelyagriculture (livestockgrazing)• Remnant dredgertailings from historicgold mining, some ofwhich was removed forNew Don Pedro Projectconstruction31

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR1301201104000 cfs water elevation (ft)9000 cfs water elevation (ft)Roberts Ferry Bridge10090Hickman BridgeElevation (ft)807060State Rte 99Santa Fe Ave BridgeSRP 6CHAPTER 250403020Slope< 0.0003Slope< 0.00150 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42Miles Upstream of the San Joaquin RiverFigure 2-15. Tuolumne River water surface profile generated by the 1969 USGS channel capacity study. Note that thedistance are from the floodway length, not the low water channel length, thus differ from commonly used river mileagemarkers.factors combined to produce a variable, dynamic,and complex channel morphology. However, withinthis local variability, consistent morphologicalpatterns emerge that can be related to habitatrequirements of aquatic organisms, and thereforeused to formulate restoration objectives. Thisinterplay between local variability (complexity),general planform, and cross-sectional pattern isextremely important to habitat structure.There is limited information describing thenatural channel morphology of the TuolumneRiver prior to the arrival of European settlers.While Native Americans did occupy the TuolumneRiver watershed, their interactions with theriver had much less impact than actions initiatedin the late 1840’s with the California Gold Rush.The best characterization of the historical channelmorphology would therefore come prior to 1848,but no information exists from this era. The 1854plat maps, accompanying survey notes, verbalaccounts, and lithographs contained in the“History of Stanislaus County” (Branch 1881)provide some glimpse of channel morphology.However, our first documented characterization ofthe river corridor comes from Soil ConservationService’s 1937 aerial photographs. Considerablegold mining, grazing, and agricultural encroachmenthad already occurred for many years prior tothis photographic series. The main differencebetween channel conditions observed in 1937photographs and conditions in later years is thatflow regulation and storage in the upstreamwatershed was more recent, and the landscapehad therefore not been appreciably disturbed byflow and sediment regulation. Much of theanalysis of natural channel conditions relies onthe 1937 photographs.The fundamental building block of alluvial riversis the alternate bar unit (Dietrich 1987), composedof an aggradational lobe (depositionalfeature) and scour hole (the “pool”) (Figure 2-16). The submerged portion of the aggradationallobe is commonly called the “riffle”, whereas theexposed portion is labeled the “point bar”32

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORY(Dietrich 1987). With the relatively deep poolopposite the point bar, this alternate bar unit isanalogous to a riffle-pool sequence. An alternatebar sequence, comprised of two point bar units,forms a complete channel meander with awavelength roughly equaling 9 to 11 bankfullchannel widths (Leopold et al. 1964). Thestructural complexity provided by an alternate barsequence is extremely important to aquaticorganisms in the Tuolumne River, which will bedescribed later in this chapter.The idealized alternate bar sequence shown inFigure 2-16 is more common in the sand-beddedreach than the gravel bedded reach. Severalexamples of sinusoidal meanders are evident inthe sand-bedded zone (Figure 2-17), with the bestexample between RM 22 and 24 (Figure 2-18).Less stereotypical alternate bar sequences arecommon in the gravel bedded reach, and are morecomplex (Figure 2-19). Common to all manifestationof these alternate bar sequences are severalimportant components:• During low flows, the channel thalweg meandersaround exposed alternating point bars, butduring high flows, the bars submerge and theflow direction straightens. Bedload transportduring high flows occurs mostly across the barface rather than along the thalweg (Figure 2-16) (Dietrich 1987).• There is a transition from exposed, coarseralluvium in the active channel (shaded lighteron Figures 2-17 to 2-19) to finer grained sandand silts on floodplain surfaces.• Pools are usually found on the outside ofmeanders; riffles join two adjacent point barsand is the area where flowing water crosses thepath of sediment transport (crossover).• The back sides of point bars often exhibit scourchannels, termed lateral scour channels, thatprovide habitat for numerous species, includingsalmon.Historically:• Channel migration and/or avulsions leftremnant alternate bar sequences isolated fromthe new channel location during low flows(Figures 2-17 to 2-19). This mobile channelcreated sloughs and oxbows, most of which hadstanding water from groundwater seepage, andwere the focal point of large riparian forests.• Channel migration, while eroding alluvium on theoutside of the bend, deposited new alluvium onthe inside of the bend, creating new point barsand floodplains.• Years with low flows and small floods encouragedriparian vegetation to initiate on barsurfaces, but larger floods that caused point barscour and channel migration discouragedriparian vegetation from becoming permanentlyestablished on the margins of point bars.Therefore, much of the channel margin wasgently sloping into the low water channel andrelatively free of riparian vegetation. Historical channel morphology ingravel-bedded zonePrior to flow regulation, large floods, bedloadtransport, and channel migration resulted in adynamic channel morphology and diverseriparian vegetation. This dynamic quasi-equilibriumin channel form is characteristic of alluvialrivers (Schumm 1977; Knighton 1984). Barsurfaces had sparse but diverse riparian vegetation,with denser forests concentrated on sloughs,abandoned channel locations, and higher elevationterraces (Figure 2-19). Bankfull channelwidths were approximately 550 ft, identified fromfloodplain indicators on the 1937 aerial photos. Across section surveyed in 1990 (Trinity Associates)located approximately four miles upstreamof Waterford (RM 35.5) shows a clearly definedbankfull channel and floodplain surface that hasbecome fossilized (i.e., unaltered from its pastcondition by recent geomorphic activity) (Figure2-20). Using this bankfull indicator, a surveyedwater surface slope of 0.0015, and an estimatedManning’s roughness value of 0.035 to 0.040 forbankfull flow, the predicted bankfull dischargewas 10,000 cfs to 11,000 cfs. This flow equated toa recurrence interval of 1.65 year flood at the LaGrange gaging station, which compares favorablywith literature values for bankfull discharge(approximately a 1.5 year flood (Leopold 1994),and substantiates our interpretation of this featureas the pre-NDPP bankfull channel. By comparison,the 1.5- year recurrence interval flood forunimpaired conditions determined by floodfrequency analysis was 8,400 cfs, thus corroboratingfield measurements. The bankfull width onthis cross section is approximately 540 ft.Meander wavelengths in the gravel-bedded reachwere variable, with typical values near 2,800 feet,CHAPTER 233

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 2Figure 2-16. Idealized alternate bar unit, modified from Dietrich (1987) and McBain and Trush (1997)34

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORYbut occasionally reaching as long as 4,000 ft.Meanders typically had low amplitude (< 400 ft)and large radius of curvature (>1,500 ft), and thechannel form was a combination of single-threadand split channels (mild braiding) (Figure 2-19).Channel movement appears to have been dominatedby a combination of channel avulsion andchannel migration. Historical channel morphology insand-bedded zoneThe sharp transition from gravel-bedded to sandbeddedriver downstream of Geer Road (RM 24)caused a notable shift in channel morphology: inthe sand-bedded zone the channel was almostentirely single thread, and alternate bars approachedthe idealized pattern (Figure 2-18).Bankfull widths estimated from the 1937 airphotos were approximately 600 ft. Meanderwavelengths were much less variable than in thegravel-bedded zone, tending toward 3,000 ft. Theamplitude of meanders was much higher than thegravel-bedded zone, ranging from 600 ft near RM23 to 750 ft near present-day Shiloh Bridge (RM3.5). Channel movement in this zone appearstypical of Midwestern sand-bedded streams (e.g.,Mississippi River), where progressive channelmigration increased meander amplitude andsinuosity until the meander “pinched off” or “cutoff”, abandoning most of the meander and reinitiatingthe migrational pattern. This meandercutoff process created oxbow wetland and riparianhabitats that are typically highly productive areasfor many species. The lower sand-bedded sectionof the Tuolumne River is of great potential valueas a richly diverse and highly productive area tofish and wildlife production. Historical sediment supply andtransportSediment comprising the bed and banks of thelower Tuolumne River originated in the SierraNevada, and was transported downstream to theCentral Valley by winter and spring snowmeltfloods. Floods transported a wide range ofparticles, from cobbles and boulders that formedthe structure of gravel bars, to fine sands and siltsthat formed fertile floodplains. As slopedecreased from the Sierra Nevada toward theconfluence with the San Joaquin River, particlesize decreased from cobbles and boulders nearLa Grange (RM 50) to fine sand downstream ofDry Creek confluence (RM 16). Specific rates ofhistoric sediment transport were less importantthan the process itself: the critical process for thealluvial river reaches, including both sand- andgravel-bedded zones, was that sediment scouredand transported downstream from a particularlocation was replaced by sediment originatingfrom similar processes upstream. This functional“conveyor-belt” periodically transported sediment,scoured and rebuilt alluvial deposits, andover time, maintained equilibrium in the quantityand quality of in-channel storage depositsthroughout the river. This process in turn provideda consistent renewal and maintenance ofhigh quality aquatic and terrestrial habitat in thelower river. Evolution to present-day conditionsBeginning with the California Gold Rush in 1848and continuing to the present, Anglo-Europeanmanipulation of the channel morphology hascaused large-scale changes to the Tuolumne Rivercorridor (Table 2-6).After more than a century of cumulative impacts,the river has been transformed from a dynamic,alluvial river (capable of forming its own bed andbank morphology) to a river fossilized betweeneither man-made dikes, or agricultural fields, orfossilized within riparian vegetation that hasencroached into the low water channel. Riparianforests have been reduced in areal extent, andnatural regenerative processes have been inhibited.Excavation of stored bed material for goldand aggregate mining eliminated active floodplainsand terraces and left behind large inchanneland off-channel pits. Off-channel pits areseparated from the river by steep-banked dikesand dikes which confine the channel to anunnaturally narrow corridor. The loss of coarsesediment supply that historically providedessential sediment for the formation of alternatebar features and in-channel and floodplain habitatstructure, combined with the dramatic reductionin high flows, has prevented regenerative fluvialprocesses from promoting river recovery. Thesechanges are largely responsible for the currentlydegraded state of the river channel. Not only arethe ingredients for a healthy channel no longeravailable to the river (sediment supply), but theprocesses are handicapped or absent (high flowregime and natural variability within hydrographcomponents).CHAPTER 235

CHAPTER 2TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR36Ft.Figure 2-17. 1937 example alternate bar sequence in sand-bedded reach near the San Joaquin River confluence (RM 4.5), showing a rapidly migratingalternate bar morphology and large tracts of riparian vegetation. Note conversion of riparian vegetation to agricultural use is well underway.

37Ft.Figure 2-18. 1937 example alternate bar sequence in sand-bedded reach immediately downstream of the gravel-to-sand bedded transition (RM 23),showing more consistent alternate bar morphology.CHAPTER 2LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORY

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 2Ft.Figure 2-19. 1937 example alternate bar sequence in gravel-bedded reach, near 7/11 Materials plant site at RM 38.The effects of these changes are illustrated bycomparing 1937 photos with 1993 photos. In thegravel-bedded zone, the impact of aggregateextraction is well illustrated: historic floodplainswere mined to depths far below the river thalweg,and the resultant pits are separated from the riverby dikes constructed of either gravel or topsoil(Figure 2-21). In downstream reaches from RM35.0 to 24.0, in-channel aggregate extraction pitswithin the low water channel range up to 38 ftdeep and 400 ft wide. Reduction in the magnitudeof flood-peaks has caused the low water channellocation to remain nearly constant over time. Thepreviously dynamic channel and point bar on thenorth bank in Figure 2-21, and elsewhere, havenot changed since 1937 and have rarely beenmobilized since 1970 as a result of the reducedhigh flow regime. Leading edges of point barsthat were previously free of mature vegetaton, arenow encroached by a thick band of willows,buttonbush, and alders. In upstream reaches wheredredgers operated across the valley, the unnaturaland fragmented channel location has not changedappreciably since 1937 (Figure 2-22).Changes to the sand-bedded reaches are similar,but resulted from agricultural and urban encroachmentrather than aggregate extraction. Conversionof the riparian corridor to agriculture and urbanuses reduced floodway width, and introducedbank protection that functionally halted channelmigration (compare Figures 2-17 and 2-18 toFigures 2-23 and 2-24). Reduced peak flows alsoinhibit channel migration.2.3. ATTRIBUTES OF ALLUVIALRIVER ECOSYSTEM INTEGRITYAlthough the ecological integrity of the TuolumneRiver has suffered, there is considerable opportunityto improve the river corridor by re-establishingcritical fluvial geomorphic processes. Butdefining, let alone restoring, a riverine ecosystemis challenging. We hypothesize that the fundamentalAttributes of river ecosystem integrity aredefined by the physical processes that create andmaintain the ecosystem form or physical structure.Based on our interpretation of historicalconditions on the Tuolumne River (assumed to38

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORYapproach undisturbed conditions), and literaturedocumentation of natural fluvial processes in otheralluvial rivers, we developed a list of “Attributes ofAlluvial River Ecosystem Integrity.” This approachwas useful in developing quantitative rehabilitationobjectives on the Trinity River in NorthernCalifornia (McBain and Trush 1997), which can beapplied to the Tuolumne River. Restoring thesecritical Attributes, within boundaries defined bysocietal constraints, is essential for improving thehealth and productivity of the Tuolumne River.Because the river behaves differently between thegravel-bedded zone and the sand-bedded zone,several Attributes are unique to each reach.ATTRIBUTES OF ALLUVIAL RIVER ECOSYS-TEM INTEGRITYATTRIBUTE No. 1. Spatially complex channelmorphology.No single segment of channelbed provideshabitat for all species, but the sum of channelsegments provides high-quality habitat fornative species. A wide range of structurallycomplex physical environments supports diverseand productive biological communities;ATTRIBUTE No. 2. Streamflows and water qualityare predictably variable.Inter-annual and seasonal flow regimes arebroadly predictable, but specific flow magnitudes,timing, durations, and frequencies are unpredictabledue to runoff patterns produced by stormsand droughts. Seasonal water quality characteristics,especially water temperature, turbidity, andsuspended sediment concentration, are similar toregional unregulated rivers and fluctuate seasonally.This temporal “predictable unpredictability”is a foundation of river ecosystem integrity;ATTRIBUTE No. 3. Frequently mobilizedchannelbed surface.In gravel-bedded reaches, channelbed frameworkparticles of coarse alluvial surfaces are mobilizedby the bankfull discharge, which onaverage occurs every 1-2 years. In sand-beddedreaches, bed particles are in transport much ofthe year, creating migrating channel-bed“dunes” and shifting sand bars.CHAPTER 2110Left bank looking downstreamRight bank105Mixed stands of very old cottonwoodsRelative Elevation (ft)10095Old black willow12/8/1989 ground surfaceNarrow leafwillow9012/8/1989 water surface (100 cfs)Pre-NDPP bankfull channel, approx. 10,000 cfs1969 flood elevation (38,600 cfs)1997 flood elevation (approx. 60,000 cfs)85-600 -500 -400 -300 -200 -100 0 100 200 300Distance (ft)Figure 2-20. Cross section at RM 35.5 showing fossilized pre-NDPP bankfull channel and floodplain surface ingravel-bedded reach.39

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORATTRIBUTE No. 4. Periodic channelbed scour andfill.Alternate bars are scoured deeper than theircoarse surface layers by floods exceeding 3- to 5-year annual maximum flood recurrences. Thisscour is typically accompanied by re-deposition,such that net change in channelbedtopography following a scouring flood usuallyis minimal. In gravel-bedded reaches, scour wasmost likely common in reaches where high flowswere confined by valley walls;ATTRIBUTE No. 5. Balanced fine and coarsesediment budgets.River reaches export fine and coarse sediment atrates approximately equal to sediment inputs.The amount and mode of sediment storagewithin a given river reach fluctuates, butsustains channel morphology in dynamic quasiequilibriumwhen averaged over many years. Abalanced coarse sediment budget impliesbedload continuity: most particle sizes of thechannelbed must be transported through theriver reach;Table 2-6. Land uses and effects on the lower Tuolumne River from 1848 to present.CHAPTER 2Land Use Time Period Location Disturbance Effect on channelPlacerMiningUrbanGrowth1848-1880 La Grange andUpstream (RM50)1850-presentModesto toWaterford (RM15 to 30)Turned over floodplainsand terraces; spoilplacement on fertileareasNeed for commerciallumber, space andaesthetic valueDestroyed natural channel morphology,increased sediment supply,destroyed instream habitat, removedriparian forestsConfined river corridor (reducedwidth), constructed dikes, removedriparian vegetation, increasedpollution loading into riverDredgerMining1880-1952 Roberts Ferryto La Grange(RM 38 to 50)Turned over entireriparian corridor valleywallto valley-wall; spoilplacement on fertileareasDestroyed natural channel morphology,increased sediment supply,destroyed instream habitat, removedriparian habitatGrazing 1850-present San Joaquinconfluence toLa Grange (RM0 to 50)Farming 1860-present San Joaquinconfluence toLa Grange (RM0 to 50)Young riparianvegetation is grazed,water sources becomefeces conduitsMature and establishingriparian vegetationis cleared. Channellocation stabilizedDestabilized banks, discouragednatural riparian regenerationConfined river corridor (reducedwidth), constructed dikes, removedriparian vegetation, increased pollutionand fine sediment loading into riverFlowRegulation1890-presentDownstream ofLa Grange (RM0 to 52)Magnitude, duration,frequency, and timing ofhigh flow regime isaltered and reduced,reduced/eliminatedsediment supply fromupstream watershedBed coarsening and downcutting,fine sediments accumulated inchannel, channel fossilized byencroaching riparian vegetation,channel migration and bar buildingvirtually eliminated, floodplainconstruction and deposition reduced,quantity and quality of instream andriparian habitat greatly reducedAggregateMining1930-presentHughson to LaGrange (RM 24to 50)Large instream and offchannel pits, dredgertailing removalHistoric floodplains are left as deepponds, floodway narrowed by dikesseparating ponds from river, riparianvegetation is cleared, regeneration isprevented and mature standseliminated.40

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORYCHAPTER 2Ft.Figure 2-21. 1993 example alternate bar sequence in gravel-bedded reach, near 7/11 Materials plant site at RM 38,showing aggregate extraction on historic floodplain surfaces and confinement of contemporary floodway with dikesand encroached riparian vegetation. Compare to Figure 2-19.ATTRIBUTE No. 6. Periodic channel migrationand/or avulsion.The channel migrates at variable rates andestablishes meander wavelengths consistent withregional rivers with similar flow regimes, valleyslopes, confinement, sediment supply, andsediment caliber. In gravel-bedded reaches,channel relocation can also occur by avulsion,where the channel moves from one location toanother, leaving much of the abandonedchannel morphology intact. In sand-beddedreaches, meanders decrease their radius ofcurvature over time, and are eventually bisected,leaving oxbows;ATTRIBUTE No. 7. A functional floodplain.On average, floodplains are inundated onceannually by high flows equaling or exceedingbankfull stage. Lower terraces are inundated byless frequent floods, with their expected inundationfrequencies dependent on norms exhibited bysimilar, but unregulated river channels. Thesefloods also deposit finer sediment onto thefloodplain and low terraces;41

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 2Ft.Figure 2-22. 1950 photo of dredger tailings upstream of Roberts Ferry (RM 43), showing that the channel location has not appreciably changed from 1950to 1993.42

43Ft.Figure 2-23. 1993 example alternate bar sequence in sand-bedded reach near the San Joaquin River confluence (RM 4.5), showing agriculturalencroachment, loss of floodplain, and loss of riparian corridor. Compare to Figure 2-17.CHAPTER 2LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORY

CHAPTER 2TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR44Ft.Figure 2-24. 1993 example alternate bar sequence in sand-bedded reach immediately downstream of the gravel-to-sand beddedtransition (RM 23), showing agricultural and urban encroachment on point bars. Compare to Figure 2-18.

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORYATTRIBUTE No. 8. Infrequent channel resettingfloods.Single large floods (e.g., exceeding 10-yr to 20-yrrecurrences) cause channel avulsions, rejuvenatemature riparian stands to early-successionalstages, form and maintain side channels, andcreate off-channel wetlands (e.g., oxbows).Resetting floods are as essential for creating andmaintaining channel complexity as lessermagnitude floods, but occur less frequently;ATTRIBUTE No. 9. Self-sustaining diverse riparianplant communities.Based on species life history strategies andinundation patterns, initiation, maturation, andmortality of native woody riparian plants culminatein early- and late-successional standstructures and species diversities (canopy andunderstory) characteristic of self-sustainingriparian communities common to regionalunregulated river corridors;ATTRIBUTE No. 10. Naturally-fluctuatinggroundwater table.Groundwater tables within the floodway arehydrologically connected to the river, andfluctuate on an inter-annual and seasonal basiswith river flows. Groundwater and soil moistureon floodplains, terraces, sloughs, and adjacentwetlands are supported by this hydrologicconnectivity.Attribute number 2 (variable flow regime) iscentral to all physical and ecological processes,thus causes many of the other attributes. The needto emphasize annual flow variation warrants thisdistinction as a separate attribute. The usefulnessof all Attributes is derived by their ability todefine desired conditions and quantifiable channelrehabilitation goals. Attribute No. 9 is the only“biological” attribute, and is included because ofthe interactions of hydrologic and fluvial processeswith riparian vegetation.The biological benefits of these geomorphicallybasedrestoration actions are discussed in thefollowing sections.2.4. BIOLOGICAL RESOURCES2.4.1 Riparian resourcesA discussion of riparian vegetation within theTuolumne River corridor must be premised on thebiological and physical processes that perpetuateriparian vegetation. The term “riparian” describesa unique physical environment and associatedplant vegetation along banks of freshwater bodies,watercourses, estuaries, and surface-emergentaquifers and adjacent areas. Streamflows andgroundwater in these areas provides soil moisturesufficiently in excess of that available throughlocal precipitation, rendering these areas capableof supporting vegetation that requires moderateamounts of water (Warner et al. 1984). The extentof groundwater influence therefore defines theriparian corridor width and the plant assemblagesthat grow there.California riparian corridors are uniquelydominated by winter deciduous hardwood trees,which can only survive within the microclimaticand edaphic (soil and soil moisture) conditionswithin the riparian corridor (Robichaux 1977).Riparian vegetation patterns and species commontoday are remnant of the last ice age, in whichhigher precipitation supported these plants inupland habitats as well as along river bottoms.During the last 15,000 years, what we know asriparian vegetation in the Central Valley hasbecome restricted to river corridors, and nowgrows only within the approximate 100-year floodlimits (Katibah 1984). The interaction betweenplant species and the physical environmentcreates spatially complex, heterogeneous vegetationassemblages.The complexity and heterogeneity of riparianvegetation renders their classification cumbersome;in the past, the predominant classificationschemes were “communities” and “associations.”However, the term “community” has not beenuniversally defined, implies artificial boundariesand interactions (e.g., that each community isindependent of adjacent communities), and alsoincludes animal populations . “Associations”assume that certain species associate with eachother, within site-specific conditions, and oftencannot be expanded to other locations.CHAPTER 245

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 2To avoid problems associated with these classificationsystems, the Restoration Plan uses the“plant series” classification system based onSawyer and Keeler-Wolf (1995). This systemaccommodates the natural patchiness along theTuolumne River. Plant series consist of repeatingpatches of vegetation, usually comprised ofmultiple species, but always having one or twospecies that dominate. Series are stratified intocanopy, shrub, and ground layers, with the seriesname determined by the species of greatestrelative abundance within the highest strata(Sawyer and Keeler-Wolf 1995). The list of plantspecies comprising the stand defines the compositionof a particular plant series.Individual riparian plant species typically havefour life-cycle stages: initiation, establishment,maturity, and senescence (Figure 2-25). Thesestages are defined as follows:1. Initiation begins after a seed lands onexposed, moist substrate and germinates; thisstage continues through the first growingseason.2. Establishment begins after the firstgrowing season and continues until theplant has enough resources to begin sexualreproduction.3. Maturity begins when a plant first flowersand produces seeds.4. Senescence follows maturity, when seedproduction and reproductive capacity decline.The morphology of riparian stands is a result ofhydrologic, climatic, and fluvial processesinteracting with the life history of individualspecies. Over time, these processes vary mortalityrates at each life stage, resulting in variable anddynamic riparian stands. For example, a particularyear may exhibit high seedling mortalityassociated with a high flow scouring flood, whilelater, more moderate floods may encourageseedling survival on certain bank surfaces. Fluvial processes and riparian lifehistoryRiparian stands of the pre-1850 Tuolumne Rivercorridor were created and maintained by complexinteractions between the physiologic tolerances ofeach plant species and the dominant physicalprocesses, which includes:• hydrologic: magnitude and timing of flowinundation, and groundwater table fluctuation;• fluvial geomorphic: channel morphology (scourchannels, sloughs, floodplain/terrace elevations),channel migration and avulsion, finesediment deposition on floodplains andterraces, point bar scour, and woody debristransport.Hydrological processesAnnual streamflow patterns and riparian plantlifecycles interact to produce a dynamic relationshipbetween (1) mortality caused by surface orgroundwater inundation or dessication and (2)survival when adequate soil moisture conditionscorrespond to seed availability. High flows thatexceed the bankfull stage inundate floodplainsand recharge groundwater tables in floodplains,oxbow lakes, and sloughs. Historically, the timingof spring snowmelt floods coincided with seedreleasetiming of most woody riparian species(May-July), so when floodplain, oxbow, andslough surfaces were moist, airborne seeds landedand germinated on these surfaces. Point barsurfaces, generally at lower elevations thanfloodplains, were inundated during seed dispersal,which prevented germination.Occasionally, long duration spring snowmeltfloods had deleterious effects on certain riparianplants. Plants typically breath through their roots,but when roots are underwater they becomedeprived of oxygen, causing considerable stress tothe plant. Plants respond to inundation, coldtemperatures, and short photo period by goinginto dormancy. This increases their survival.Fremont cottonwood and white alder haveevolved pores in their bark called lenticels, whichincrease gas exchange to the plant during longterminundation, increasing their resistance.Fremont cottonwoods and white alders tend tobreak dormancy earlier than willows, and thislonger growth period benefit gives them anadvantage over willows. Under natural conditions,the longer growing season for cottonwoodsand alders, combined with willows being moresusceptible to scour mortality because theytypically grow closer to the main channel,resulted in a more equal distribution of species.Loss of winter scouring floods and long-durationinundation snowmelt floods has favored willowspecies (particularly narrow-leaf willow) andreduced natural regeneration of cottonwoods,reducing riparian species diversity and complexity.46

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORYSpring snowmelt floods rose and fell gradually.After the peak, river water levels declined graduallythrough summer months (Figures 2-4 to 2-8,and 2-10). In some years oxbow lakes and sloughsdried up completely, requiring plant roots to followreceding moisture down into the soil column. Someplant species evolved rapidly growing roots tofollow the dwindling sub-surface soil moisture(Segelquist et al. 1993). During summer months,soil moisture gradients caused by varying elevationsrelative to the groundwater table createdstrong selective pressures on vegetation. Thesegradients, combined with local soil differences,caused distinctive zonation patterns in riparianCHAPTER 2Figure 2-25. A generalized riparian hardwood life cycle showing life stage, and mortality agents that affect lifestages.47

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 2vegetation. In many locations, plants initiated butwere later unable to survive because of insufficientsoil moisture. Desiccation mortality may preventinitiation for many successive years, causingdistinct age classes between successful riparianstand cohorts.Fluvial geomorphic processesChannel migration and avulsion are typicallyconsidered undesirable because migration oftenresults in damage or loss to human structures.However, channel migration (Attribute #6) was acritical process for riparian regeneration and largewoody debris introduction into the channel.Alluvial channels typically migrate across theriver valley by eroding the outside of the meanderbend and undercutting mature riparian forests.This process historically introduced woody debris,which added structural complexity to instreamhabitat (Figure 2-26). Additionally, bank erosionon the outside of the bend was balanced by bardeposition and floodplain formation on the insideof the bend (Figure 2-26). Fine sedimentsdeposited on the inside of the bend are ideal seedbeds, and if hydrological conditions provideadequate moisture, new initiating bands ofriparian vegetation advance along the buildingbar. This process is best illustrated historically inthe sand-bedded reaches, where scroll bars offiner sediments caused banding of emergentriparian vegetation on the inside of meanderbends (Figure 2-17). In the gravel-beddedreaches, substrates were coarser and drainedbetter. Consequently, riparian forests werehistorically much more extensive in the lowerriver.In sand-bedded reaches, large floods typicallyspread out over the valley and did not causelarge-scale and rapid change in channel location;rather, meander evolution and eventualcutoff were the primary avulsion processes.These meander-bend cutoffs usually left eithersloughs or oxbow lakes, and because theyinitially provided clean seed bed surfaces andconstantly moist condition, riparian regeneration(Figure 2-27) quickly occured there.An example of the dynamics of natural rivers is depicted above. (A) A channel with adequate space to migrate(Attribute 6) erodes the channel bank on the outside of the meander bend during high flows (Attribute 2), (B)encouraging aged riparian trees to topple into the channel (Attribute 9). (C) A deep pool also forms here, whichprovides structural complexity (Attribute 1) for good fish habitat. As bank erosion continues, the pool “migrates”downstream (Attribute 6), but high quality habitat is maintained. (D) On the opposite bank, high flows(Attribute 2) scour and redeposit coarse sediments (Attributes 4 and 5), forming a shallow bar on the inside ofthe meander bend (Attribute 1), and providing clean spawning gravels. (E) This area, in turn, provides idealslow-water rearing conditions for juvenile chinook salmon, as well as habitat for aquatic insects (fish food),amphibians and reptiles. (F) Progressively higher up the gravel bar surface, a dynamic interplay occurs betweenreceding water levels during the spring snowmelt (Attribute 2), and the presence of riparian tree seeds(Attribute 7). These woody riparian trees are sporadically scoured out (Attribute 8), and those established highenough on the bank are toppled into the channel as the channel migrates back across the valley (A).Figure 2-26. Conceptual role of channel migration in creating spatially and temporally complex riparian corridorhabitat.48

49Ft.Figure 2-27. 1937 photo at the confluence of the San Joaquin River, showing oxbows and scroll-bars, bank erosion, and the range of riparian ageclasses. Undisturbed floodplains and low terraces supported lush riparian forests. Note conversion of riparian vegetation to agricultural use iswell underway.CHAPTER 2LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORY

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 2In gravel-bedded reaches, channel avulsion andfloodplain disturbance typically occurred duringlarge floods (>5 to 10-year recurrences on theannual maximum series). Channel relocationappears to have been rapid, perhaps occurring inmany locations within a single flood event.Additionally, larger floods scoured and redepositedsediment around trees, logs, and shrubson floodplains and low terraces, which createdsloping, undulating, floodplain surfaces. Thisfloodplain morphology led to considerablevariation in soil and drainage conditions, andprovided diverse plant species (each with differentphysiological tolerances) a broad range ofmicrohabitats in which to survive (Strahan 1984).However, these larger floods also caused mortalityto the riparian community, primarily in thesteeper, more confined gravel-bedded reach.Typically, the closer to the low water channel ariparian plant initiated, the higher the risk ofscour mortality. Conversely, the farther from thelow water channel, the higher the risk of desiccationmortality. Channelbed scouring floodshistorically prevented riparian hardwood encroachmentinto the active channel and kept point barsrelatively free of riparian vegetation (Figures 2-17to 2-19). Seedlings initiating close to the summerlow water edge have shallow roots and areparticularly susceptible to channelbed surfacescour, and moderate winter flood events typicallykill over 90% of the plants that survive the firstgrowing season (McBain and Trush 1997).Floods caused scour mortality not only on younggenerations of trees, but also on mature andsenescent trees. As floods progressively inundatedfloodplain surfaces with greater depths,woody debris in transport would accumulate onmature and senescent stands with force greatenough to topple trees. In some cases, a group oftrees may have been removed in a domino effect,leaving bare holes in a stand where new initiationcould occur. Historically, the large volume ofwoody debris derived from the upper watershedprior to dam blockage would have had significanteffects on riparian stand structure.Figure 2-28. Conceptual historical cross-section near Shiloh Bridge (RM 3.5). Riparian vegetation occurs acrossentire cross section, and is concentrated in oxbows (historic channel locations) and scour channels. Note tree sizenot to scale.50

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORYLarge floods also deposited considerable volumesof fine sediment on floodplains, and less frequentlyon terraces, creating seed beds thatencouraged riparian initiation. New fine sedimentdeposits imported nutrients, improving plantgrowth and regeneration on floodplain andterraces. Again, initiation success also dependedon local soil moisture conditions. To avoidsuffocation from deep silt and sand deposited atthe base of established plants, many speciesdeveloped the ability to sprout adventitiousroots further up the trunk, closer to the newdepositional surface, to preserve gas exchangefunctions.Each woody riparian species and life stageresponds differently to hydrologic and fluvialprocesses, but particular plant life stages aremore vulnerable to the effects of flow variationand fluvial processes. Initiating and early establishingplants are especially susceptible tomortality agents because substrate compositionand water availability are vital during early lifestages. If they survive the summer, they aresusceptible to scour-induced mortality duringrelatively small winter and spring floods. Once theplant escapes a two to four year window anddevelops deeper and more extensive root system,the risk of mortality decreases. Ultimately,mortality to maturing plants depends on channelmigration, being pushed over by flood debris, ordisease. These periodic and spatially variabledisturbance patterns and mortality agents perpetuatethe plant series diversity historically foundalong the Tuolumne River. Pre-settlement riparian vegetationcompositionPrior to the gold rush era, the riparian corridorextended miles wide in places where the riverlacked confinement. Pre-settlement riparianvegetation in the sand-bedded reaches wascomparable to a lush jungle “gallery forest” wherelianas (vines) connected the canopy to denseundergrowth (Bakker 1984) (Figures 2-17, 2-27,2-28). Throughout the corridor, western sycamore,Fremont cottonwood, Oregon ash, andCHAPTER 251

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 2valley oaks grew in profusion on floodplains andterraces, while willows and alders grew alongactive channel margins. In mature riparian stands,clematis, grape, and poison oak lianas drapedfrom the canopy to the ground. An estimated13,000 acres of riparian vegetation occupied theLower Tuolumne River from La Grange toModesto (RM 19-52) before widespread Europeansettlement in the 1850’s (Katibah 1984). Ingravel-bedded reaches, relatively sparse riparianvegetation was restricted between bluffs, andflourished in high flow scour channels andabandoned main channels where soil moistureconditions were optimal and flood effects wereminimal (Figure 2-19).Diversity in plant series and stand structure wasmaintained by the dynamic interaction betweeninitiation and maturation on one hand, andmortality on the other. Dominance of one speciesover another was kept in check by variablemortality agents provided by dynamic hydrologicand fluvial processes. This struggle between plantphysiological tolerances and fluvial and hydrologicprocesses resulted in noticeable patterns inspecies location on specific geomorphic surfaces.Riparian plants have been shown to initiate andestablish after floods of specific recurrenceintervals (Bradley and Smith 1984; Osterkampand Hupp 1984; Auble et al. 1994). The riparianinventory (presented in Chapter 4) and crosssections through riparian vegetation (Figure 2-20)suggest that these relationships historicallyexisted on the Tuolumne River (Table 2-7). Impacts of land use on riparianvegetationAt present, less than 15% of the historicalriparian forests remain along the Tuolumne River.Human alteration of riparian vegetation began withNative American harvest and fire management, buthuman manipulation intensified with placer goldmining in the late 1800s, followed by dredgemining, flow and sediment regulation, urbanencroachment, agricultural encroachment, grazing,and aggregate extraction (Table 2-6). Miningactivities and urban/agricultural encroachmentdirectly removed large tracts of riparian vegetation(compare Figures 2-17 to 2-19 with Figures 2-21 to2-24); other land uses were less direct. For example,livestock selectively graze younger riparian plants,which severely limits riparian initiation.Flow and sediment regulation indirectly impactedriparian vegetation on the Tuolumne River bymodifying the hydrologic and fluvial processesthat influence survival and mortality of riparianvegetation. Each increment of flow regulation (LaGrange Dam, Hetch Hetchy Dam, Old Don PedroDam, New Don Pedro Dam) successively reducedthe magnitude, duration, and frequency of floodflows, and removed key mortality agents (scour,channel migration, flood toppling, and inundation).Reduced flood scour allowed riparianvegetation to initiate along the low water channel,where historically they would have been scouredout. As vegetation matured, extensive rootsystems anchored alluvial deposits to functionallyfossilize historically dynamic alluvial features. Thisprocess has been documented on rivers with largeupstream storage reservoirs (Pelzman 1973), and iscommonly referred to as riparian encroachment.Prior to flow regulation, riparian vegetationperiodically encroached onto active channelsurfaces (e.g., during drought), but large floodseventually scoured these geomorphic surfaces,causing mortality to much of the encroachedvegetation. Large storage reservoirs eliminatedTable 2-7. Rlationships between established riparian plant series, flood frequency, and streamflow for the lowerTuolumne River corridor based on cross section surveys and GIS analysis.Plant SeriesRecurrence Interval rangePre-NDPPMagnitudes (cfs)Post-NDPPMagnitudes (cfs)Narrow-leaf willowsummer baseflow to 1.5 yearflood 150 to 8,500 150to 3,020White alder/ Box elder 1.5 year to 5 year flood 8,500 to 25,000 3,020 to 7,500Fremont Cottonwood 5 year to 20 year flood 25,000 to 51,000 7,500 to 12,800Valley oak 20 year to the 100 year flood 51,000 to 89,000 12,800 to 18,00052

4000Sand-bedded zoneGravel-bedded zone350030001937199353Width of Riparian Corridor (ft)2500200015001000500San JoaquinRiver00 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 5River Mile (RM)Figure 2-29. Riparian corridor widths in 1937 and 1993, starting at the Tuolumne River’s confluence with the San Joaquin River (RM 0.0) and ending just upstream of theNew La Grange Bridge (RM 51.5).CHAPTER 2River exitsfoothillsLINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORY

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 2large floods, allowing encroached riparian standsto mature and senesce, forming uniformly agedstands. Additionally, when larger floods do occur,the minimal loading of woody debris is insufficientto topple trees. Lastly, because damsfunctionally trap all sediment from the upperwatershed, flood flow releases scour away ratherthan deposit fine sediment (fine sands and silt),thus discouraging vegetation initiation oncontemporary surfaces.To illustrate changes to the riparian corridorwidth, we examined 1937 and 1993 aerialphotographs to measure the extent of riparianshrub and tree vegetation every half mile, for theentire Tuolumne River corridor (Figure 2-29).Valley width, which defines the historic ripariancorridor, was also plotted. By 1937, extensivedisturbance had already reduced riparian vegetationto a small fraction of its prior extent, andfurther reductions between 1937 and 1993. Nearthe confluence of the Tuolumne River with theSan Joaquin River at RM 5.5 (formerly theMcClesky Ranch), the 1937 riparian forests onthe southern bank exceeded 120 acres; theseforests were reduced to 30 acres by 1993. Thisevolution is illustrated by the conceptual crosssections near Shiloh Bridge (compare Figure 2-28 with 2-30). Channel migration (and woodydebris input) has decreased from reduced flowsand bank rip-rap. The functional riparian corridorwidth has also been reduced as farmable land wasmaximized by “reclaiming” the riparian corridor.Vegetation that once extended from bluff to bluffprior to the gold rush era is now confined to anarrow band (yards wide) along the activeFigure 2-30. Conceptual existing cross-section near Shiloh Bridge (RM 3.5). Riparian vegetation is restricted to anarrow band along the low water margin, and grows on what were open point bars before dam closure in 1971.54

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORYchannel in many locations (Figure 2-21) or isaltogether nonexistent.Changes to riparian vegetation directly affectmicroclimate, nutrient availability, habitat qualityand diversity (Gregory et al. 1991). Loss ofchannel migration and clearing of valley oaks andcottonwoods in the riparian corridor decreasedlarge woody debris recruitment, reduced woodyplant cover along the river corridor, encouragedexotic plants to infiltrate into the riparian zone,and increased ambient temperatures within theriver corridor. In reaches where the riparian zonehas been less disturbed, Fremont cottonwood andvalley oak stands have become senescent, whileyounger willow, alder and box elder stands areencroaching along the low flow channel. Thisevolution has contributed to simplifying thechannel morphology. Riparian encroachment hastransformed channel margins from shallow, lowvelocity, exposed cobble habitat (high qualityhabitat for chinook rearing) to deeper, highervelocity habitat. Summary of riparian resourcesPast and present land use practices combined withstreamflow and sediment regulation transformedthe Tuolumne River corridor from an alluvial riversystem in dynamic quasi-equilibrium, to a semistaticriver channel. This transformed environmentscarcely resembles ecological conditions towhich riparian vegetation, salmonids, and otherwildlife species adapted; as a result, riparianhabitat area and species diversity has declineddramatically. The following section examines theCHAPTER 255

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 2relationship between salmon habitat and lifehistory, exploring cause and effect relationshipsbetween changes in fluvial processes and salmonpopulation stability.2.4.2. Chinook salmon2.4.2.1. Life historyChinook salmon, Oncorhynchus tshawytscha, arethe largest of the five North American Pacificsalmon species, occasionally weighing over 90pounds, although most adults weigh from 10 to40 pounds. Chinook are anadromous andsemelparous (die after spawning once), with twobehavioral forms: one designated as “stream-type”and the other as “ocean-type” (Healey 1991).Ocean-type chinook are typical of populations onthe Pacific coast south of British Columbia, as onthe Tuolumne River. In general, ocean typesmigrate to sea during their first year of life,usually within four months after emerging fromthe spawning gravels, spend most of their oceanlife in coastal waters, and return to their natalriver in the fall to spawn. Presently, fall-runchinook salmon constitute the most abundantanadromous run in the Sacramento/San JoaquinRiver system (Yoshiyama 1998), and support thebulk of ocean harvest.Most chinook salmon return to spawn in freshwaterstreams when they are between two and fiveyears old. The two-year-old grilse (precociousmales and females that prematurely migrate backinto the river) are abundant in some years, butCentral Valley runs are now comprised mostly ofthree-year-olds. Four- and five-year-old fish wereonce far more common than at present. Thegradual decrease in the average age and size offish in the Central Valley runs is a result of heavycommercial ocean fishing (EA 1992).The life-cycle of the chinook salmon begins andends on the spawning grounds (Figure 2-31). Inthe San Joaquin basin, adults typically arrive atthe spawning grounds from October into December,peaking in early to mid November. Spawningtakes place from mid October through lateDecember. Duration of incubation varies dependingon water temperature, but generally extendsfor 60-90 days. Alderdice and Velson (1978)report that time to 50 percent hatching rangedfrom 159 days at 37 o F to 32 days at 61 o F. Winterwater temperatures on the Tuolumne Rivertypically range between 48 o F and 60 o F. AlevinsFigure 2-31. Life cycle of the Tuolumne River fall-run chinook salmon, showing how major stages in their life historyrelate to typical annual runoff patterns. The unimpaired average annual hydrograph for WY 1996 is used as example.56

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORYremain in the gravel for two or three weeks afterhatching, absorbing most of their yolk sac beforeemerging as fry into the water column. Fry emergemostly from January to March.Fry (length50 mm) generallyleave the Tuolumne River in April or May andenter the ocean as smolts between April and July.Hatton and Clark (1942) trapped emigrating fryand juveniles in fyke nets at Mossdale in the SanJoaquin delta from 1939-1941. Their data suggestbimodal peaks in emigration, with one peak inFebruary and another in April. Several factorsmay determine the timing of fry and juvenilemigration, and whether fry and juveniles rear inriveror continue downstream. Some researcherssuggest that fry migration is related to flowmagnitude. Kjelson et al. (1981) observed peakseine catches of chinook fry in the Sacramento/San Joaquin Delta correlated with increases instreamflow from storm runoff. Other authorsspeculate that social interaction or densitydependentmechanisms cause fry to be displaceddownstream (Lister and Walker 1966; Reimers1968; Major and Mighell 1969). Roper andScarnecchia (1999) report that timing of smoltemigration was significantly related to streamtemperature and phase of the lunar cycle, but notdischarge. All of these factors likely interact toplay a variable mechanistic role in the downstreamdistribution of fry from the TuolumneRiver, depending on flow, habitat availability andcondition, and population density.A small portion of the chinook salmon juvenilepopulation produced annually may remain toover-summer in the Tuolumne River and thenemigrate as yearlings to the ocean in winter or thefollowing spring (EA 1992). This rare, butpotentially important, life history strategy on theTuolumne River is most likely controlled bywhether summer/fall water temperatures aresuitable for fish survival.Pacific salmon form local populations withgenetic variation maintained by adaptations toenvironmental conditions (Taylor 1991). Adaptationsarise as evolved characteristics of the speciesthat are inherited by each individual from thepreceding generations as behavioral, physiologicalor developmental responses to changingenvironmental conditions. Adaptive responsesmodify the behavior or morphology of the organismto improve its relationship to the environmentand maximize the survival and fitness of theindividual. Considerable adaptive variability insalmonids has apparently evolved since glacialrecession within the last 15,000 years (Taylor 1991).Preliminary information from genetic studies onCentral Valley chinook salmon indicate differencesbetween seasonal runs but little divergence amongfall-run stocks (Nielsen et al. 1994; Banks et al.1996) However, more comprehensive geneticevaluations are in progress that could revealpossible genetic differences in fall-run chinooksalmon from the Tuolumne River and other CentralValley streams.Environmental conditions to which chinooksalmon are adapted include:• a variable flow regime that inundated differentsegments of the channelbed with differenttiming, frequencies, depths, and velocities;• a structurally and topographically diversechannelbed, providing habitat for variousspecies and life stages at most flows;• interactions with the biological community thatprovided invertebrate food resources, and whichincluded competitive or predatory interactionswith other fish and wildlife species.The following sections describe hydrologicconditions, habitat conditions, and communityinteractions that provided historical environmentalconditions within which chinook salmonevolved. Along with an historical context,contemporary conditions are also described, usingavailable data, photo series, and general ecologicalprinciples. Constraints limiting production andsurvival of chinook salmonPhysical alteration of the channel morphology,dams and flow regulation, and elimination ofcoarse sediment supply have cumulativelydegraded chinook salmon habitat in the gravelbeddedreaches. The once dynamic and complexTuolumne River channel has become static,providing less in-channel, floodplain, andriparian habitat than the historic channel provided(Table 2-8).In response to the degraded conditions andrequirements mandated by the NDPP license, theDistricts conducted a multi-year research programCHAPTER 257

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORTable 2-8. Major impacts to chinook salmon habitat and population levels resulting from alterations to historicalhydrologic and fluvial geomorphic processes.Changes in hydrology, fluvialgeomorphology, or channel morphologyReduced frequency and magnitude of peak flowsReduced baseflowsImpacts to chinook salmon life history or habitatReduced frequency of spawning gravel turnover and cleansing,resulting in reduced survival of eggs and alevins.Riparian fossilization of alluvial deposits and concurrent loss ofrearing habitat along margins of point bars.Disruption of immigration/emigration patterns, particularly duringjuvenile and smolt emigration.Reduced spawning gravel availability.Higher concentration of pesticides and fertilizers from agriculturalreturn flows.Increased superimposition of redds resulting in significant eggmortality.CHAPTER 2Loss of upper watershed areasLoss of coarse sediment supply and transportLoss of Large Woody Debris (LWD)Reduced access to spawning and rearing habitats, reducingproduction potential.Reduced nutrient supply, reducing production potential.Reduced spawning habitat quantity and quality.Reduced exposed bars, reducing rearing habitat along lateral barfeatures.Coarsening of bed surface, reducing spawning habitat quality.Reduced nutrients supply and habitat structural diversity.Loss of fine sediment transport capacityIn-channel gravel extraction and gold dredger miningOff-channel gravel extractionto assess chinook salmon population dynamicsand habitat conditions in the lower TuolumneRiver. The study approach attempted to identifypotential physical and biological limitations tochinook salmon production, specifically factorsthat limited salmon production levels (EA 1992).Potential limiting factors (ecological constraints)identified include:• reduced spawning gravel availability, and eggmortality from superimposition of redds;• poor spawning gravel quality causing low eggsurvival-to-emergence;• inadequate streamflow during fry and juvenileemigration;Accumulation of in-channel fine sediment storage reduced adultholding habitat and emergence success.Infiltration of fine sediments into spawning gravels decreasesemergence success.Increased imbeddedness of surface particles degrades fry rearinghabitat.Reduced spawning and rearing habitat area.Increased habitat availability for non-native fish species that prey onjuvenile salmon, reducing smolt out migration success.Reduced ability of river to route coarse sediment through reaches,decreasing spawning and rearing habitat.Confinement of floodway and prevention of channel migration,reducing spawning and rearing habitat.Loss of riparian habitat, floodplain, and gravel recruitment asfloodplains are mined and banks are armored.• reduced and degraded rearing habitat;• increased in-river predation by non-native fishspecies;• increased Bay/Delta and ocean mortality(striped bass predation, delta pumpingmortality, sport/commercial harvest);• elevated in-river and Bay/Delta watertemperatures.Additional research (CDFG 1998) has alsoindicated that significant juvenile and smoltmortality may occur in the sand-bedded reaches,potentially related to predation and/or unfavorablewater temperatures.58

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORYCHAPTER 2Figure 2-32. Conceptual cross section through a spawning riffle to show the effects of flow variation on distributingspawning area to lateral margins of the channel. Hydrologic conditions andchinook life historyAdaptive responses to the hydrologic regime werecritical elements molding chinook life historystrategies. Not only did streamflow and floodsform and maintain instream habitat, but chinooksalmon also adapted to the natural variability inmagnitude, timing, duration, and frequency ofstreamflow events. Although only relatively smallportions of their lives are spent in the riverenvironment, these life stages are criticallyimportant to the population.We analyzed unregulated hydrograph componentsto examine historical flow patterns with significanceto chinook salmon life history adaptations.These conditions were then compared to thecurrent hydrologic conditions set by the FERCNDPP license amendment in the SettlementAgreement.Immigration and spawning. Chinook salmonimmigration and spawning occurred during fallbaseflows and fall storms of low magnitude andshort duration. Unimpaired average fall baseflowsranged from 332 cfs to 542 cfs during CriticallyDry and Extremely Wet water years, respectively,and frequently exceeded 1,000 cfs during wetterwater year types. Variability in streamflow duringthe spawning season, combined with diversechannel topography, provided variation in depthand velocity that was an important mechanism todistribute spawning within different channellocations. This mechanism maximized availablespawning habitat (Figure 2-32), and probablyreduced scour and superimposition mortality onincubating eggs.Minimum streamflows during the spawningseason are now determined by the FSA flowschedule (Table 2-5), which sets steady, nonfluctuatingflow releases, and does not incorporatehistorical streamflow variability. The effectsof flow regulation on the hydrograph duringspawning can be seen by comparing representativeunimpaired and regulated water years (Figure 2-33). Regulation of fall baseflows at unnaturallylow streamflows may produce the undesirableconsequence of limiting spawning to the center ofthe channel as opposed to margin habitat (Figure2-32), encouraging salmon to construct theirredds on top of pre-existing redds (redd superimposition),and increasing the vulnerability of eggpockets to scour during moderate or large floods.59

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR10,000A9,0008,000CHAPTER 2Discharge (cfs)Unimpaired fall floods7,0006,0005,0004,0003,0002,0001,00001-Oct 8-Oct 15-Oct 22-Oct 29-Oct 5-Nov 12-Nov 19-Nov 26-Nov 3-Dec 10-Dec 17-DecDate10,000B9,0008,000Discharge (cfs)7,0006,0005,0004,000Regulated "chinook attraction flows"Regulated "chinook spawning flows"3,0002,0001,00001-Oct 8-Oct 15-Oct 22-Oct 29-Oct 5-Nov 12-Nov 19-Nov 26-Nov 3-Dec 10-Dec 17-DecDateFigure 2-33. Daily average flows during chinook Salmon spawning (Oct. 1 to Dec. 20) for: A) typical unimpairedWY 1947-1956, and B) typical regulated WY 1973-1982. Variability in the unimpaired flow regime may have been animportant mechanism for distributing spawning habitat to different locations within the active channel.60

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORY20,00018,000Daily Average Discharge (cfs)16,00014,00012,00010,0008,0006,0004,0002,0000Extremely WetNormalCritically DryCHAPTER 21-Sep11-Sep21-Sep1-Oct11-Oct21-Oct31-Oct10-NovDay of Year20-Nov30-Nov10-Dec20-Dec30-DecFigure 2-34. Magnitude and timing of the first fall storms of each water year of record, showing minimal differencesbetween water year classes.The magnitude and timing of fall storms wereevaluated to determine the effects of these eventsin encouraging or disrupting chinook emigrationand spawning patterns. Fall storms may be animportant trigger for upstream migration. Thefirst flood pulses after the summer low-flowmonths also may have been an importanthydrograph component to remove fine sedimentsfrom spawning gravels (Lisle 1989). Unimpairedfall storm magnitudes ranged between 1,400 cfsand 16,000 cfs for Critically Dry and ExtremelyWet years, respectively (Figure 2-34). The naturalvariability in fall hydrographs has been eliminatedby the FSA flow schedule requirement of a45-day steady spawning flow, and has beenreplaced by a single “fall attraction pulse flow”ranging up to 2,500 cfs and lasting only 2 or 3days.Egg incubation and development. Twohydrograph components, winter baseflows andwinter floods, occur during egg incubation anddevelopment. Winter baseflows perform essentialfunctions of oxygen delivery and waste removal.Winter storms represent a potentially significantmortality agent if the channelbed (and redds)scours to the depth of chinook egg pockets.Unimpaired baseflows during incubation (Oct-16to Mar-31) ranged between 775 cfs and 2,800 cfsfor Critically Dry and Extremely Wet water years,respectively. Flood magnitudes during incubationand emergence included the entire range ofunimpaired winter floods determined by floodfrequency analyses (Table 2-3), and rangedbetween 3,400 cfs and 23,000 cfs for dailyaverage floods during Critically Dry and ExtremelyWet water years, respectively. Unimpairedpeak flows occasionally exceeded 100,000 cfs(1862, 1956, 1997). Winter flood magnitudes arepresently regulated by NDPP operations with theArmy Corps of Engineers (ACOE) allowing amaximum discharge of 9,000 cfs at Modestobelow Dry Creek, although releases have been upto 10,400 cfs at La Grange and flows havereached 12,000 cfs at Modesto, excluding the1997 flood. Flood releases in the upper gravelbeddedreaches can be substantially lower forshort periods when unregulated streamflows fromDry Creek are high.61

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 2Juvenile rearing and emigration. Fry and juvenilerearing patterns were likely related to winterbaseflow magnitudes and timing. Water yearswith consistent baseflows and lower magnitudeflood peaks enabled more fish to rear in upstreamreaches near the spawning grounds. Water yearswith more variable flows and larger magnitudewinter and spring snowmelt flood peaks probablydistributed fry and juveniles downstream to lowersand-bedded reaches of the Tuolumne River, theSan Joaquin River, and Bay/Delta estuarinerearing habitats, where historically high qualityrearing habitat existed.Smolt emigration was directly tied to snowmeltrunoff and instream temperature conditionsbeginning in late March and continuing throughJune. By this time most chinook had left the riversystem. Higher spring outflows during wetteryears probably extended the in-river duration ofrearing by providing cold water temperatures intolater summer months: July, August and evenSeptember of some years. Downstream migrationinto the Bay/Delta and the ocean was a pivotalstage in the life history of chinook, as they weremore vulnerable to high temperature and predation.High spring runoff reduced predation onemigrating juveniles by reducing downstreammigration time and by lowering temperatures(discussed in greater detail in subsequent sections).High flows also increased turbidity, whichreduced predation efficiency by sight feeders (e.g.,black bass). The average peak discharge forsnowmelt runoff ranged between 4,500 cfs and13,000 cfs for Critically Dry and Extremely Wetwater years, respectively, with median peakmagnitudes in excess of 20,000 cfs. Additionally,the combination of Tuolumne, Merced, Stanislausand San Joaquin River flows significantly increasedthe magnitude of streamflow through theBay/Delta. The timing of the spring snowmeltflood peak was related to snowpack magnitude(the wetter the snowpack, the later the peak), andvaried from early May in Critically Dry years tomid-June for Extremely Wet years (Figure 2-10).The importance of high spring flows duringoutmigration on smolt survival has been shownfor the Tuolumne River (USFWS 1987; Kope andBotsford 1990; USFWS 1992; EA Engineering1997; CDFG 1998) and for other Central Valleyrivers as well (SPCA 1997). Studies on theTuolumne River under FERC-mandated 1971 and1986 study plans determined which factorsinfluenced the rate and magnitude of changes inpopulation size of the San Joaquin systemchinook salmon. The severity of mortality duringsmolt outmigration was inversely related todischarge. They hypothesized that high springdischarge reduced mortality by reducing watertemperature, reducing predation by increasingturbidity and water velocity, diluting pollutants,and reducing the proportion of smolts entrainedin delta water export facilities.The link between streamflow volume duringchinook smolt outmigration and survival torecruitment is a fundamental issue in CentralValley chinook salmon and water management.The relationship between spring flows, in-riverrearing and outmigration conditions, and the rateand magnitude of changes in population size ofSan Joaquin River chinook salmon, was exploredby use of a statistical model developed (EA 1992,1996). The model incorporates both densityindependentmortality influenced by spring flows,and density-dependent mortality represented by aRicker-type spawner-recruit relationship. Themodel shows that spring flow correlates closelywith escapement and is a key factor in thedramatic fluctuations in chinook salmon populationlevels. Mechanisms responsible for theRicker spawner-recruit relationship, in whichadult chinook escapements beyond a thresholdprogressively reduce recruitment of juveniles intothe population, will be discussed in more detailbelow.Additional evaluations relating springstreamflows to smolt survival are currently beingconducted by CDFG and TRTAC. The CDFGstudy evaluates the entire Tuolumne River andSan Joaquin River, and includes portions of theBay/Delta extending to Chipps Island at the headof Suisun Bay (CDFG 1998). TRTAC studies arealso evaluating the relationship between smoltsurvival and spring streamflow in discrete reachesof the Tuolumne River, and specific restorationproject reaches. Preliminary results indicatejuvenile and smolt survival are low during lowspring runoff conditions, and survival is poor inthe Mining Reaches. Habitat conditions and chinook lifehistoryAlluvial rivers are typically hot-spots ofbiodiversity (Tietje et al. 1991; Stanford et al.1996) and may support core fish populations62

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORYwhich serve as stable population sources for redispersalin response to local extinction(Lichatowich et al. 1995). Within alluvial reachesof the Tuolumne River, local habitat complexitywas historically maintained by high rates ofenergy and material input, storage, and transport;increased corridor width as the river emergedfrom confined canyon reaches into the valley, andconsequent increased nutrient inputs fromadjacent riparian vegetation; higher seasonalvariability in streamflow and temperature; and thepresence of nutrient-rich floodplain soils(Stanford et al. 1996). Without pre-settlementdescriptions of physical habitat, we analyzedchannel and floodplain habitat structure on thespatial complexity provided by the alternate barchannel morphology. Alternate bars are theprimary geomorphic units of alluvial rivers andrepresent the fundamental habitat template for allfreshwater life stages of chinook salmon and forother species (Figure 2-36). The 1937 aerial photoseries also proved useful. The topographicdiversity of the channelbed and active bar surfacesprovide a diversity of habitat for chinook salmon,including:• adult holding in pools during immigration;• preferred spawning substrate and physicalmicro-environment (depth and velocity);• high quality egg incubation environment inspawning gravels;• winter and spring rearing in slack water alongbar surfaces, and in shallow backwater zonesbehind point bars;• summer (yearling) rearing in pools, riffles andruns;• fry and juvenile refugia during floods oninundated bar and floodplain surfaces;• abundant food production areas;• large organic debris load (large wood) thatprovided habitat structural diversity and habitatfor fish and aquatic invertebrates.Immigration and spawning. As discussed earlier,the alternate bar is composed of an aggradationallobe and a scour pool (Figure 2-16). The outsideof the meander is the location of the pool or slowmovingrun. A meandering channel erodes banksand undercuts trees (cottonwood, alder) providingtree and rootwad woody debris input into theriver, which increases pool habitat complexity(Figure 2-26). Pools provide velocity shear zones,and cover from turbulence, undercut banks,depth, shade, large boulders, bubbles, and woodydebris. Additionally, pools may provide temperaturerefugia when ambient temperatures arecritically high.CHAPTER 270,000Fall run chinook salmon escapement60,00050,00040,00030,00020,00010,000019461948195119531955195719591961196319651967196919711973197519771979198119831985198719891991199319951997YearFigure 2-35. Historical chinook salmon escapement estimates, showing trends in population booms and crashes.63

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 2Figure 2-36. Idealized alternate bar sequence showing location of habitat features used by chinook salmon.64

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORYSuitable bed material and hydraulic conditionsat the pool-riffle transition (pool-tail) provideideal spawning conditions for salmon. Gravelstored in pool tails and riffles are subject tohigher frequency of scour and redeposition,and these patches of gravel are consequentlywell-cleaned and sorted to a size class preferredby spawning salmon. Scour and fillprocesses can remove fine sediment anddiscourage embeddedness or armoring of thesurface layer, facilitating redd excavation bythe chinook salmon female. Additionally, waterinflow associated with zones of acceleratingwater velocity (at pool-tails) creates higherintragravel flow, facilitating oxygen deliveryand waste removal from salmonid egg pockets.Spawning gravel availability. Habitat suitable forspawning on the Tuolumne River is finite,imposing an absolute limit on production at somelevel. A 1986 estimate of spawning habitat (EA1992) enumerated 72 riffles and 2.9 million ft 2 ofriffle area (at 230 cfs). By assuming all riffle areawas spawnable (a generous assumption), and aspawning area requirement of 216 ft 2 for eachspawning pair, the study concluded that theavailable spawning gravel in the Tuolumne Riverbelow La Grange dam would provide between10,000 and 13,500 spawning sites, at 230 cfs.These studies concluded that spawning habitatwas a significant factor limiting salmon production.Redd mapping at riffle 3A (Figure 2-37)shows the clumped distribution and superimpositionof redds in the riffle and pool tail, withspawning concentrated near the stream margins.Increased flows would inundate progressivelymore spawning area along the point bar adjacentto the riffle, potentially reducing superimposition.CDFG has recommended experimenting withflow variability as a way to distribute spawnersand help reduce redd superimposition. Districtstudies (EA 1992) also recommended implementingmanagement activities to distributespawners more evenly throughout the spawningreaches and reduce superimposition.Comparisons to historical conditions are impossiblebecause historical data estimating spawningareas and spawning riffle conditions are unavailable.In addition, reaches that were relativelyundisturbed in the 1937 aerial photo sequences(RM 25-40) have since been dramatically alteredby aggregate extraction. In contrast, upstreamreaches affected by gold dredger mining in theearly part of the century (RM 47-50), were subsequently“reconfigured” following removal ofdredger tailings for NDPP construction. Thesereaches are now more productive spawningreaches than under degraded channel conditionscaused by dredge mining.The alternate bar morphology at RM 38 is one ofthe best examples available showing an historicallydynamic channel morphology (Figures 2-19and 2-38), to which contemporary conditions canbe compared. These alternate bars provided avariety of habitat for chinook: fry rearing habitatalong channel margins; fry and juvenile refugia inbackwaters, lateral scour channels, and oninundated bars during floods; spawning habitat atpool-tails and riffles; and adult holding habitat indeep pools and in turbulent areas. The riverthalweg crossed the aggradational lobes betweenthe two upstream point bars, creating riffle 31,and then again forming riffle 32. At the downstreamedges of point bars, backwater zonesprovided rearing and refugia for chinook, as wellas habitat for riparian and wildlife species.We used the 1950 aerial photo sequence tocompare past spawning habitat use with contemporaryhabitat use. Escapement during the 1950spawning season was an estimated 30,000 adultchinook, a relatively high escapement year. In the1950 photos, riffle 31 is a distinct, heavilyspawned area, conservatively estimated to be50,000 ft 2 . Based on a conservative estimate of thearea of spawning habitat required, 216 ft 23 perspawning pair (Burner 1951; EA 1992), riffle 31in 1950 could have accommodated at least 231redds. Visual count of redds at riffle 31 directlyfrom the aerial photos ranged from 42-140 redds.3Burner (1951) provided an “average area of fall-run chinookredds” (54 sq ft) and an “area recommended for eachspawning pair” (216 sq ft), noting that the spatial requirementsfor each spawning pair may exceed the area of the completedredd. Burner noted that wherever sufficient spawners werepresent to utilize virtually all available spawning habitat, areasurrounding the redd amounted to three times the aareaoccupied by the redd. Burner thus suggested that aconservative estimate of the number of salmon a stream couldaccommodate could be obtained by dividing the area suitablefor spawning by four times the average area of a redd. TheCDFG (1990) Central Valley Salmon and SteelheadRestoration and Enhancement Plan suggests the average sizeof chinook salmon redds is approximately 165 sq ft, and theterritory required for a spawning pair to range between 200and 650 sq ft, but suggest the seasonal requirements forminimum spawning area per female is 75-100 sq ft.CHAPTER 265

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 2Figure 2-37. Location of salmon redds in riffle 3A (RM 49.4), showing use of riffle and pool tail habitat forspawning, and a preference for lateral (margin) zones. Redd superimposition is indicated where redd boundariesoverlap. (from EA 1992)Figure 2-21 shows the planform morphology ofriffle 31 in 1993. The previously dynamic pointbar has become fossilized by riparian vegetationencroachment. Rearing habitat along the shallowmargins of the bars is reduced to narrow stripsbetween the wetted channel edge and the encroachedvegetation. Many of the backwaterhabitats present in Figure 2-38 are either severelydegraded by warm water temperatures and waterhyacinth, or are gone. Along the south bank, entirefloodplains and terraces were eliminated byaggregate extraction. These surfaces werereplaced with pond habitat, separated from thechannel by steep-banked dikes protected fromerosion with rip-rap.Previously high quality and heavily used spawninggravels in riffle-31 have been reduced inoverall quantity and quality:• Estimates of spawning habitat availability forR31 from 1986 aerial photos (EA 1992)quantified only 25,000 ft 2 of available spawninghabitat. Field measurements conducted in 1999estimated only 4,500 ft 2 of suitable spawninghabitat at 277 cfs. (McBain and Trush andStillwater Sciences 2000) indicate a loss ofmore than half the spawning area, from 50,000ft 2 to 25,000 ft 2 of available spawning habitat.• The average “high” redd count from reddsurveys conducted from 1981 to 1995 for R31(CDFG) was 6.8 redds per year.A similar analysis of available spawning habitatwas extended to 11 riffles in the reach betweenRM 35.5 and 40.2 (Table 2-9). Spawning gravelutilization was estimated from 1950 photos forthose 11 riffles with visible spawning activity, andthen compared to spawning gravel estimates from66

67FtFigure 2-38. Aerial photograph from March 1950, showing the alternate bar sequence at RM 38.0, including point bars, scour pools, backwater areasand spawning riffles R31 and R32.CHAPTER 2LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORY

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 21986 aerial photos (EA 1992). Most riffles showedtrends similar to riffle 31: an average 43% reductionof available spawning habitat in response toimpeded bedload supply, confinement of thechannel by aggregate mining and dikes, scour andloss of existing gravels, agricultural encroachment,and riparian encroachment. Bed coarsening fromthe lack of gravel particles has also reduced theoverall quality of the remaining available habitat.Additionally, quantifying spawning habitat fromaerial estimates of spawning gravel or riffle areahas considerable limitations, because it assumesthat all available gravel within a riffle is suitable forspawning.Because no information is available to documentthe spawning habitat conditions in the rest of theTuolumne River prior to major channel alteration(1850), we can only speculate that changes tospawning gravel quantity and quality are likelycomparable along the entire river corridor: slowattrition of riffle area by fossilization of alluvialfeatures, degradation by fine sediment infiltration,loss of usable spawning habitat by coarse sedimentsupply deficit and consequent coarsening ofthe channelbed particles.The January 1997 flood had additional impacts onspawning gravels, particularly in the reacheswhere dikes, bridges, and agricultural encroachmenthave narrowed the floodway. Entire riffles(e.g., 1A, 1C, 6, 9B, 11, and others) were scouredand redeposited downstream, creating long, deepruns followed by steep riffles unsuitable forchinook spawning. Scour and mobilization of thechannelbed is beneficial to spawning gravelsubstrates, but only if sediment is available fromupstream sources to redeposit, maintaining thedynamic quasi-equilibrium in scour and depositionvolumes discussed earlier. Lack of inchannelgravel storage and supply resulting fromdams and bedload impedance reaches has slowlydepleted available spawning habitat. In the absenceof gravel introduction and channel rehabilitation,this process will continue to further degradespawning habitat.Redd superimposition. The effects of reducingthe available spawning gravel quantity and qualitywere documented by the Districts (EA 1992,Appendices 6, 7, 8) by assessing the distributionof spawners in the lower Tuolumne River, thedegree and effects of superimposition within fiveintensively studied riffles in the upper river, andegg and alevin survival. Their conclusion wasthat lack of gravel supply, combined with chinookbehavioral preferences for spawning in theuppermost reaches of the Tuolumne River, causedsubstantial superimposition of redds, even in lowescapement years. Superimposition was identifiedas the primary mechanism of density-dependentmortality, and resulted in the Ricker spawnerrecruitrelationship. These studies concluded thatsuperimposition is a significant source of mortalitybased on the following information:• The 2.9 mile-long section 1A (between Old LaGrange Bridge, RM 50.5, and Old BassoBridge, RM 47.6) was the most heavily usedspawning section, receiving an average of 53%of the spawners in surveyed sections. Yet thissection contained only about one-fifth the totalspawning gravels (673,600 ft 2 ). In 1985 at anescapement of 40,000 (the largest spawning runsince NDPP), an estimated 11,476 femalespawners used Section 1A, whereas Section 3(RM 25 to 34) contained 821,000 ft 2 of spawninggravel, but was relatively little used.• In 1988, at a relatively low escapement of 6,300adults, an estimated 1,457 females spawned insection 1A, and superimposition resulted in anestimated 20% destruction of eggs. Of the 384redds identified in the 5 study riffles during the1988 spawning season, 169 redds (44%) werebuilt on top of pre-existing redds (Figure 2-37).• Maximum production for the Tuolumne Riverwas estimated to occur at an escapement of15,000 adults. Beyond this escapement,additional spawners actually decreased productionbecause of superimposition-inducedmortality. This resulted in a Ricker-typespawner-recruit relationship. This estimate mayin fact be too high, considering the spawninghabitat attrition that has occurred since 1988,and the questionable assumption that the entireriffle area is suitable for spawning.Egg incubation and development. Gravel quality isa key determinant in successful salmonid embryoincubation and emergence (Harrison 1923; Hobbs1937). Historically, good quality spawninggravels were maintained in the Tuolumne River bya dynamic equilibrium in fine and coarse sedimentsupply and routing. Frequent scour andredeposition of bed sediments periodicallyremoved fine sediments from spawning gravelsand deposited them on floodplain surfaces. Gravelquality is now severely degraded in the Tuolumne68

Table 2-9. Comparison of estimated riffle and spawning areas from 1950 photos with contemporary (1986) conditions in the Tuolumne River Corridor.69LOCATION ESTIMATED RIFFLE AREA (FT 2 )(RM)RIFFLE 1950 1986PERCENTREDUCTION28A 40.2 24,696 29,887 0% 114 8.428B 39.5 26,460 10,381 61% 123 8.429 39.1 56,448 43,994 22% 261 1330B 38.5 35,280 13,496 62% 163 830C 38.4 35,280 21,326 40% 163 031 38.0 86,436 25,033 71% 400 6.433 37.7 56,448 29,472 48% 261 6.734B 37.5 42,336 8,005 81% 196 6.136B 36.5 63,504 53,974 15% 294 4.137 36.2 28,224 25,207 11% 131 3.338 35.5 76,356 26,316 66% 354 5.9AVERAGE 48,315 26,099 43% 224 6** Based on area recommended for each spawning pair of 216 sq ft from Burner (1950).1950 ESTIMATEDREDD CAPACITY**CHAPTER 2AVERAGE "HIGH" RCOUNT 1981-199LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORY

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 2River, because fine sediments have accumulated inthe low flow channel. Elimination of coarsebedload supply from upstream reaches by LaGrange Dam, reduction of scouring and channelformingflows, increased inputs of fine sediments(particularly from Gasburg Creek), and reducedfrequency of flows that deposit fine sediments onthe floodplain, have all contributed to the poorquality of spawning gravels.The Districts assessed gravel quality of eightriffles in 1987 and 1988 (EA 1992), by analyzingthe particle size distribution of 72 McNeil gravelsamples in riffles prior to spawning and in reddsafter the fry had emerged. The particle sizedistribution was then used to predict egg survivalto-emergenceusing the methods of Tappel andBjornn (1983). The results poor spawning gravelquality and survival to emergence in the TuolumneRiver. The average predicted survival forbaseline spawning gravels (prior to spawning)was 16 percent. The average predicted survival inredds increased to 34 percent. The increase wasdue to the effects of spawning fish cleaning finesediment from the gravel during redd construction.These estimates were then corroborated bysurvival estimates determined by emergencetrapping of chinook salmon redds in 3 riffles in1989, which, in conjunction with length-fecunditydata provided by CDFG (Loudermilk et al. 1990),showed average survival of 32 percent, andranged from 0 to 66 percent.Gravel quality analysis was also performed at 20riffle sites in the upper 15 mile spawning reach bythe Department of Water Resources (DWR 1994).The study employed non-standardized bulksampling methods for sediment removal byexcavating underwater samples with a shovel, amethod that may underpredict fine sedimentfraction because an unquantifiable portion of thefine sediment fraction may be lost during excavation.They concluded that existing gravel in theassessed reaches is “generally adequate to supportchinook salmon spawning”. For the 20 combinedsamples analyzed (surface and subsurfaceparticles), the percentage of fine sediment finerthan 1.2 mm averaged 5.8%.Rearing and emigration. Chinook salmon fryemerge from the gravels during winter monthswhen high magnitude floods historically occurred.Evidence suggests that some chinook fryemigrated to the San Joaquin River and Deltashortly after emergence, or were displaced thereby high flows or unfavorable temperature conditions.Rearing also occurred in the lower sandbeddedreaches and on the spawning grounds(gravel-bedded reaches) (EA 1997).The margins of point bars and backwater zonesdownstream of point bars generally providesuitable depth and velocity conditions, substratecomposition and cover, and an abundance ofbenthic and terrestrial invertebrate food resources.Figures 2-17, 2-18, and 2-27 show historicalalternate bar sequences in the sand-bedded zone.The key feature of the alternate bar morphology isthat as river stage increases, the water’s edgeprogressively migrates up the point bar, leaving aband of suitable habitat along the stream marginat any stage, until the water surface elevationexceeds the point bar elevation and the entire barinundates. The point bar and floodplain are thusimportant habitat refugia for rearing juvenilesduring higher flood stages.Contemporary conditions have changed riverchannel morphology considerably, particularlydue to the effects of agricultural and urbanencroachment onto floodplains and lower barsurfaces (Figures 2-21, 2-23, and 2-24). Shallowrearing habitats along stream margins have beenreduced or replaced with lower quality, deepermargin areas with poorer depth/velocity profiles.Additionally, vegetative encroachment andriparian berm formation along river banksprevent the river from progressively expandingonto lateral bars and wide, flat floodplains asriver stage increases, and fry and juveniles may beless able to access high flow refugia. This may inturn decrease survival by forcing juveniles andsmolts to rear in the lower sand-bedded reaches,the San Joaquin River, and in the Bay/Delta. Biological interactions and chinooklife historyPredation by introduced species of bass may be adominant source of mortality under low flowconditions for juvenile chinook in the TuolumneRiver (EA 1992). Smolt survival studies conductedby CDFG in 1987 at 600 cfs estimated that69% of 90,000 smolts released in the upperTuolumne did not survive the 3-day migrationto the San Joaquin river confluence. Onehypothesized mechanism for this mortality waspredation. The Districts conducted a pilotstudy in 1989 and a full study in 1990 todetermine (1) predator densities (largemouth70

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORYand smallmouth bass) in the lower TuolumneRiver and (2) rates of predation on juvenilechinook salmon by largemouth and smallmouthbass, the primary predator species.The highest concentrations of largemouth basswere found in the special-run-pools (SRPs) whichare former in-channel aggregate extraction pits.Abundance estimates ranged as high as 181 bassin SRP 2, located immediately below the primaryspawning reaches. Predator abundance in Section1 (RM 25-52) was higher than in Section 2 (RM0-25), and densities (abundance per acre or bankmile) were considerably higher in run-pool unitsthan in special-run-pool units, although confidenceintervals were also much broader. Based onestimates for each of these habitat types, thelargemouth bass population extrapolated for theentire 52 mile river was estimated to be 10,130 ±5,164 (95% confidence interval) (EA 1992).Predation rates for largemouth and smallmouthbass were low or undetected during March/Aprilsampling, but increased dramatically for bothspecies in Section-1 SRPs during a May pulseflow release. The mechanisms for this increaseare unknown. Conservative predation rateestimates were 1.0 and 3.6 salmon per day forlargemouth and smallmouth bass, respectively.Based on 1990 population estimates, largemouthand smallmouth bass could have consumed morethan 17,000 smolts per day during emigration,enough to explain the disappearance of anestimated 60,000 CWT smolts lost in the 1987study.The studies concluded that reduced predation maybe the mechanism by which high spring flowsincreased smolt survival and increased recruitment.Increased flow reduces the time smolts areexposed to predators, increases turbidity whichinhibits the predator feeding efficiency, reducesthe concentration of predators in main channelareas by forcing them into warm-water refugia,and reduced the chronic thermal stress to whichsmolts are subject at higher temperatures (discussedin greater detail below). Recent CDFG andTRTAC research also indicates that spring flowsare related to smolt survival (CDFG 1997; CDFG1998).The smallmouth bass population could not bereliably estimated due to low capture rates, butsmallmouth bass are known to begin feeding atlower water temperatures than are largemouthbass, and therefore may have an equally significant(or greater) impact on juvenile salmon aslargemouth bass. In addition to largemouth andsmallmouth bass populations, several otherpredator species are known to occur in the lowerTuolumne River, with (presumed) smallerpopulations that collectively could also impactjuvenile salmon cohorts; striped bass (Moronesaxatilis), Sacramento pikeminnow(Ptychocheilus grandis) and potentially catfishspecies. Other limiting factorsBay/Delta and ocean factors. Two additionalfactors, high juvenile mortality in the Bay/Deltaand at Delta pumping plants, and sport/commercialocean harvests that deplete adult stocks, havesignificant detrimental effects on adult escapements.Modeling studies for the Districts, basedon experimental data collected by CDFG, indicatethat up to 44% of chinook salmon juvenilesemigrating down the San Joaquin river between1973 and 1988 died because of entrainment inCVP and SWP facilities (EA 1992). USFWSstudies support these conclusions (USFWS 1987).Mitigation measures currently proposed oralready implemented, such as installing the OldRiver barrier, and reduced pumping duringemigration, should significantly reduce Bay/Deltamortality.Ocean harvest directly reduces chinook escapements.Harvest management thus represents apowerful tool for increasing the population ofreturning spawners. This aspect of salmonpopulation management is especially crucialduring low escapement years when small increasesin the escapement size are magnified dueto the lower adult/fry/juvenile densities andconsequent higher survival levels.Temperature. The effects of high water temperatureson chinook spawning, rearing, and emigrationremain less well known than other limitingfactors, yet high temperature at times may be asignificant factor limiting the chinook populationin the Tuolumne River and in the time spent inthe San Joaquin River and Bay/Delta. TheSNTEMP temperature model, developed for the52-mile lower Tuolumne River, is capable ofpredicting 5-day average instream temperaturesthroughout the year (EA Engineering 1992,Appendices 17-19).CHAPTER 271

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 2High water temperatures during rearing and smoltemigration are perhaps the most significant damrelatedhabitat alteration (apart from flow reductionand sediment blockage) in the Tuolumne River. Forthe period 1966 to 1984 (CDFG 1987), flows in Mayduring smolt emigration were less than 5,000 cfs atLa Grange in 13 of 19 years, and 8 of these 13 yearshad median water temperatures at Vernalis (on theSan Joaquin River) exceeding 67.6 ºF (19.7 ºC).These temperatures were characterized by Rich(1987) as resulting in high chronic thermal stress.A study by Brett (1952) used chinook salmon fromthe Dungeness hatchery in Washington, anddetermined a range of upper incipient lethaltemperatures of 73 ºF (22.8 ºC) to 77 ºF(25.0 ºC) ,and 12-hour median lethal temperatures rangingfrom 71.2 ºF (21.8 ºC) to 80.6 ºF (27 ºC), dependingon the acclimation temperatures. Watertemperatures as high as 86 ºF (30 ºC) have beenrecorded near La Grange Dam in summermonths. These high water temperatures on theTuolumne River correspond to periods when thereare few salmon in the river, but likely was thecause for the decline in “yearling” or oversummeringsalmon. Comparable temperaturestudies using San Joaquin River basin chinookhave not been conducted, but results could differfrom those obtained using northern races.Not only are the effects of high water temperaturedirect (e.g., thermal stress, mortality), but hightemperatures may also contribute indirectly toother limiting factors such as bass predation,smolt survival during emigration, spawningdistribution, and incubation success. The firstyear of the fry emergence study (EA 1992)showed much lower egg survival (1-2%) thanpredicted based on gravel quality, and wasattributed to mortality caused by high incubationtemperatures. High ocean and Bay/Delta watertemperatures have also been shown to cause eggmortality prior to the salmon entering their natalstreams. In addition, beyond the seasonal affectsof high temperatures on specific life historyphases, high daily fluctuations in water temperature(ranging from 12 to 14 ºF daily) are knownto occur at low flows.High water temperatures are also most likelyresponsible for limiting habitat of yearlingchinook salmon. Low summer flows and resultanthigh water temperatures can be lethal to summerrearing. The revised FERC flow schedulesprovide better conditions for summer rearingduring wet years, particularly in the upper reachesnear La Grange Dam. According to the SNTEMPmodel, 300 cfs in the summertime would provide15 miles of habitat with suitable summer watertemperatures for summer rearing. Current status of chinookpopulationThe San Joaquin River basin and Tuolumne Riverfall-run chinook salmon populations havefluctuated widely during the period in which runestimates are available (1940 to present), and aregenerally characterized by a series of years withhigh escapements alternating with years ofextremely low escapements (Figure 2-35). Therecent drought (1987-1992) resulted in populationlevels as low as 100 returning adults for threeconsecutive years. More recently, a succession ofwet years has improved flow conditions. Changeshave also been implemented in Delta exportoperations and ocean harvest that have probablybenefited the salmon runs. Adult escapementshave rebounded to 3,300, 7,200, and 8,800 adultspawners in 1996, 1997, and 1998, respectively.Preliminary estimates indicate that the 1999escapement will approximate 1998.While population levels appear strongly related tostreamflows, improved hydrologic conditionsalone may not restore populations to levelstargeted by AFRP and CALFED. Recent improvementsin escapement levels may suggest thatwetter years alone have the potential to restoreand maintain a viable salmon population at lowescapement levels between 1,000 and 10,000. Butto sustain escapements of 30,000 or more salmonwill probably require a combination of improvedstreamflows and physical habitat. The AFRP hasset preliminary production targets for theTuolumne River fall-run chinook salmon populationat 38,000 adults (harvest and escapement).These target production levels are based on twicethe average escapement levels attained during theperiod 1967-1991 and a reduced harvest rate. TheCALFED program has not set specific productiontargets, but their explicit goal of restoringsustainable populations of species by improvingecological conditions, and their collaboration withthe AFRP program, suggests similar objectives.72

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORY2.4.3. Fish and wildlife resourcesRestoring fundamental fluvial processes thatcharacterized the historical Tuolumne River maynot only aid in recovery and maintenance of achinook salmon population, but will also improveconditions for a wide range of native fish andwildlife species. Similar to our description of thechinook salmon’s adaptations to historicalecological conditions, other native inhabitants ofthe aquatic and riparian habitats provided by theTuolumne River are also adapted to the historically“pristine” conditions that existed prior toextensive degradation of the landscape. InCalifornia, the amphibian, bird, and mammalianspecies diversity in Central Valley riparian zonesrepresents the highest biodiversity found anywherein the state (Tietje et al. 1991). Riparianand floodplain habitats support at least 50amphibian and reptile species, 147 bird species,and 55 mammal species (Mayer and Laudenslayer1988).From their review of records dating from 1970,Brown and Ford (1992) identified 37 fish speciesoccurring in the lower Tuolumne River (Table 2-10). Of these 37 species, 14 species are native and23 species are introduced. The majority of thenon-native species are members of the sunfish(Centrarchidae, 8 species), minnow (Cyprinidae,4 species), and catfish (Ictaluridae, 4 species)families. Several of the sunfish species (primarilylargemouth and smallmouth bass) supportrecreational fisheries, while at the same time posea management concern as predators on juvenilechinook salmon.Appendix B provides a comprehensive description(with tables) listing the riparian vegetationseries and species found within the TuolumneRiver corridor, including both native and exoticspecies. A complete list of all wildlife speciespresent within the Tuolumne River corridor isbeyond the scope of this report, but can be foundwithin other sources. Important sources ofinformation include Mayer and Laudenslayer(1988), Tietje et al. (1991), California WildlifeHabitat Relationships, CDFG (1997), Verner andBoss (1980), Storer and Usinger (1963), and seethe Biological Resources Technical BackgroundReport, Appendix D of TID EA/IS (1998).Examples of wildlife species that may be found invalley foothill riparian vegetation includeensatina (Ensatina eschscholtzii), common gartersnake (Thamnophis sirtalis), warbling vireo(Vireo gilvus), ringtail (Bassariscus astutus) (CDFG1997), mule deer (Odocoileus hemionus), coyote(Canis latrans), raccoon (Procyon lotor), opossum(Didelphis virginiana), river otter (Lutracanadensis), muskrat (Ondatra zibethicus),California ground squirrel (Spermophilusbeecheyi), and striped skunk (Mephitis mephitis).Raptors, resident and migratory birds, Californiaquail (Callipepla californica), great blue herons(Ardea herodias), snowy egrets (Egretta thula),great egrets (Casmerodius albus), and blackcrownednight herons (Nycticorax nycticorax)also may be found within riparian zones (TID EA/IS 1998).Numerous threatened, endangered or specialstatus (TES) plant, bird, fish and wildlife speciesare also present within the Tuolumne Rivercorridor, and additional information is availablefrom the sources mentioned above for these TESspecies.Restoring a more natural riverine ecosystem willpromote conditions which favor native vs. nonnativespecies, improving stability in socially andeconomically valued species such as chinooksalmon, and in general promote a healthierenvironment.2.5. SUMMARYWhile advocating an ecosystem restorationstrategy, we must acknowledge that our actionswill never return the Tuolumne River to thehistorical conditions that existed prior to modernsettlement and intensified land development ofthe Central Valley. Instead, restoring physicalprocesses, such as channel-forming flows andcoarse sediment introduction and transport, areintended to be used as tools for restoring andmanaging the resources of the Tuolumne River inaccordance with other management strategies.Ecosystem restoration is by necessity experimentally-based,driven by hypotheses generated fromour understanding of the physical processes andthe adaptive responses of the biological community.Success of this approach is fundamentallydependent on adaptive management techniques toregularly evaluate successes and failures, and thenrefocus objectives.Based on our historical evaluation of hydrologicrecords, aerial photographs, cross sections, andextensive literature review, we developed theAttributes of Alluvial River Ecosystem Integrity,CHAPTER 273

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORTable 2-10. Fishes of the lower Tuolumne River observed since 1981 in TID/MID fishery studies. N=Native.CHAPTER 2Petromyzontidae - lampreysPacific lamprey, Lampetra tridentata (Gairdner, 1836)river lamprey, Lampetra ayresi (Gunther, 1870)Acipenseridae - sturgeonswhite sturgeon, Acipenser transmontanus (Richardson, 1836)Clupeidae - herringsAmerican shad, Alosa sapidissima (Wilson, 1811)threadfin shad, Dorosoma petenense (Ghnther, 1867)Cyprinidae - carps and minnowscommon carp, Cyprinus carpio (Linnaeus, 1758)goldfish, Carassius auratus (Linnaeus, 1758)golden shiner, Notemigonus crysoleucas (Mitchell, 1814)hitch, Lavinia exilicauda (Baird & Girard, 1854)Sacramento blackfish, Orthodon microlepidotus (Ayres, 1854)Sacramento splittail, Pogonichthys macrolepidotus (Ayres, 1854)hardhead, Mylopharodon conocephalus (Baird & Girard, 1854)Sacramento pikeminnow, Ptychocheilus grandis (Ayres, 1854)red shiner, Cyprinella lutrensis (Baird & Girard, 1853)fathead minnow, Pimephales promelas (Rafinesque, 1820)Catostomidae - suckersSacramento sucker, Catostomus occidentalis (Ayres, 1854)Ictaluridae - bullhead catfisheswhite catfish, Ameiurus catus (Linnaeus, 1758)brown bullhead, Ameiurus nebulosus (Lesueur, 1819)black bullhead, Ameiurus melas (Lesueur, 1819)channel catfish, Ictalurus punctatus (Rafinesque, 1918)Salmonidae - troutschinook salmon, Oncorhynchus tshawytscha (Walbaum, 1792)rainbow trout, Oncorhynchus mykiss (Walbaum, 1792)Poeciliidae - livebearerswestern mosquitofish, Gambusia affinis (Baird & Girard, 1853)Atherinidae - silversidesinland silverside, Menidia beryllina (Cope, 1866)Cottidae - sculpinsprickly sculpin, Cottus asper (Richardson, 1836)riffle sculpin, Cottus gulosus (Girard, 1854)Percichthyidae - temperate bassesstriped bass, Morone saxatilis (Walbaum, 1792)Centrarchidae - sunfishesblack crappie, Pomoxis nigromaculatus (Lesueur, 1829)white crappie, Pomoxis annularis (Rafinesque, 1818)warmouth, Lepomis gulosus (Cuvier, 1829)green sunfish, Lepomis cyanellus (Rafinesque, 1819)bluegill, Lepomis macrochirus (Rafinesque, 1819)redear sunfish, Lepomis microlophus (Gunther, 1859)largemouth bass, Micropterus salmoides (Lacepede, 1802)smallmouth bass, Micropterus dolomieu (Lacepede, 1802)Percidae - perchesbigscale logperch, Percina macrolepida (Stevenson, 1971)Embiotocidae - surfperchestule perch, Hysterocarpus traski (Gibbons, 1854)NNNNNNNNNNNNNNAll Species: 37Native Species: 1474

LINKING PHYSICAL PROCESSES AND SALMON LIFE HISTORYupon which proposed restoration objectives arebased (see Section 2.3). Restoring these attributescan occur within pre-existing humansocioeconomic and infrastructural constraints(e.g., a regulated water supply and land use withinthe river corridor), as will be shown in section 3.2regarding flood releases for channel maintenancepurposes. Restoring the Attributes will restore andhelp sustain the myriad of habitats needed tosupport the native populations that inhabit theTuolumne River, including habitats essential forsalmon production. These Attributes were used togenerate the following hydrologic and geomorphicrestoration objectives, and allowed us topredict the expected benefits to chinook salmon:A. Encourage inter-annual and seasonal flowvariability.Considering adaptations in the life history ofchinook salmon and other organisms to specificenvironment conditions will allow us to use theseadaptations to our advantage. For example,varying flows during spawning would make thebest use of available habitat by distributing fishand encouraging use of all available habitat.Restoring alternate bar sequences would providequality rearing habitat at a variable range offlows. This restoration strategy is already acknowledgedto a limited extent by the use ofspring and fall pulse flows for improvingoutmigration and immigration conditions.B. Increase the magnitude and frequency ofshort duration peak flows to initiate bedmobility and localized scour/deposition.Mobilizing bed surfaces exposes fine sediment fordownstream transport and deposition on floodplainsurfaces, which, combined with reduced finesediment supply and increased coarse sedimentsupply, should reduce fine sediment storage andincrease the quality and quantity of spawning andfry rearing habitat.Combining coarse sediment introduction withchannel reconstruction (restoring bedloadimpedance reaches) will help restore bedloadrouting downstream, thereby replenishingspawning gravels and gravel bars throughout thegravel-bedded reaches.Restoring flows of sufficient magnitude andfrequency to inundate contemporary and restoredfloodplain surfaces will deposit fine sedimentsderived from the low water channel onto floodplainsurfaces instead of in spawning gravel, andwill encourage floodplain development/processes.C. Increase the magnitude and frequency of peakflows to initiate bed scour on alluvialdeposits along the low water margin toreduce riparian encroachment.Mobilization of exposed bar surfaces will discouragefossilization of short-term alluvial deposits byreducing riparian encroachment along the lowwater channel margins, preserving these marginsfor fry rearing habitat, and maintaining theavailability of gravel/cobble storage deposits foreventual downstream routing.D. Increase coarse sediment input to balancemainstem transport capacityRestoring coarse sediment supply (particularlyspawning gravels between 8 mm to 128 mm) inthe gravel-bedded reaches will provide immediatespawning and rearing habitat, and will eventuallyroute downstream to replenish other bars.Introducing clean gravels, combined withreducing fine sediment input, will increasespawning and rearing habitat quality and quantity,increasing juvenile production.Cleaner alluvium (reduced silt and sandembeddedness) will also improve aquatic invertebratehabitat and prouctivity, the primary foodresource for juvenile salmon.E. Reduce fine sediment input into the river.Reducing fine sediment input to the river,particularly near La Grange, will improvespawning and rearing habitat conditions, andincrease the longevity of gravel quality improvementefforts.Reducing fine sediment input, combined with highflows that transport and deposit fine sedimentonto floodplain surfaces, will reduce instreamstorage of fine sediment, increase pool depth,improve spawning and rearing habitat quality, andimprove salmon emergence and rearing success.CHAPTER 275

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 2F. Reduce human encroachment onto floodplainsto allow limited channel migration.Restoring channel migration will increase input oflarge woody debris, adding to the structuralcomplexity of the channel and providing instreamcover for salmon.Restoring channel migration, combined withcoarse sediment input, will stimulate formationof gravel bars and floodplains as the channelmigrates, creating high quality salmon spawningand rearing habitats.G. Restore channel morphology, with a bankfullchannel and floodway scaled to the expectedhigh flow regime.A properly-sized bankfull channel will encouragebedload transport by contemporary flood flows,promoting scour and redeposition of on-sitealluvial deposits and rejuvenation of downstreamsites. This will help the river create and maintainhigh quality, diverse salmon habitat.A properly sized bankfull channel will encourageriparian vegetation to establish in natural locations(upper bars and floodplains), and discourageencroachment and fossilization of alluvialdeposits along the low water channel margin.A properly sized bankfull channel and floodwaywill regulate peak shear stress over a range offlows to reduce risk of catastrophic bed scour andchannel degradation (as occurred during the 1997flood). This will re-establish self-sustainingfunction to the channel, increasing longevity ofsalmon habitat restoration efforts (gravel introduction,channel reconstruction).These recommendations to restore alluvial riverintegrity are integrated with other managementoptions in developing a restoration vision andstrategy for the Tuolumne River corridor that willbest restore salmon habitat and population.Restoring coarse sediment supply, providingperiodic high flows capable of routing thosesediments, fixing bedload impedance reaches,restoring confinement to the low water channel,and providing a floodway corridor width to allowchannel migration, are essential restorationstrategies for re-establishing fundamentalhydrologic and fluvial processes. These processesform and maintain the natural channel morphologyand can do much of the work in restoring orrehabilitating instream and floodplain habitatsthat sustain healthy populations of aquatic andriparian species.76

GEOMORPHIC AND RIPARIAN INVESTIGATIONS3. FLUVIAL GEOMORPHIC AND RIPARIAN INVESTIGATIONSTo evaluate the extent that contemporary conditionson the Tuolumne River achieve the Attributesof Alluvial River Ecosystem Integrity(Attributes) presented in Chapter 2 requires somequantification of fluvial and riparian processes onthe Tuolumne River. Because this type of informationis limited or non-existent, we assessedmany of these processes during the developmentof this Restoration Plan. By comparing theactivities needed to achieve the Alluvial RiverAttributes, with constraints imposed by dams,human encroachment into the floodway, channeldegradation from past mining, etc., we can assesswhether management actions can restore theAttributes within existing constraints. Theseinstitutional constraints usually limit the ultimateextent of restoration, so a scaled-down river,combined with more intensive mechanicalmanagement to supplement this shortfall inAttributes (natural processes), may be required.The objective of this chapter is to quantify andevaluate several of the Attributes. Our evaluationof fluvial processes concentrated on the gravelbedded reach because most of the in-river factorslimiting salmon spawning, egg incubation, andrearing are in this reach. The riparian evaluationsextend throughout the 52 miles of river. Specificinvestigations included:Geomorphology and hydrology• Bedload impedance reaches• Bed mobility thresholds• Bedload transport at Basso Bridge• Fine sediment (sand) sources• Evolution of M.J. Ruddy 4-Pumps floodwayrestoration project and associated channeldesign considerations• Flood flow evaluationRiparian vegitation• Relate riparian vegetation series to hydrology/channel morphology• Corridor-wide riparian inventoryCHAPTER 377

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 33.1. FLUVIAL PROCESSES3.1.1. Bedload impedance reaches(Attribute #5)A bedload impedance reach is defined as alocation where hydraulic conditions of thecontemporary flow regime (generally less thanFLOWSmall lobe of bedload depositedsince pit was constructedChannel bedHigh flow water surfaceAbandoned extraction pitFigure 3-1. Typical bedload impedance reach, where instream aggregateextraction pit traps all bedload transported from upstream reaches.10,000 cfs) are insufficient to transport coarsebed particles through the reach. These reachesare former instream aggregate extraction and golddredger pits, where channel width, depth, andslope have been modified to the extent that allbedload in transport from upstream reachesdeposits into the pit (Figure 3-1). Reachesdownstream of the pit do not have an upstreambedload supply, and bedload is recruited from thebed itself, causing net degradation (lowering) andcoarsening (winnowing) of the bed. The entirelower Tuolumne River from La Grange Dam tothe confluence of the San Joaquin River wassurveyed to identify bedload impedance reaches.Re-establishing continuity in coarse bedloadtransport and routing is the first step to restoringa dynamic river; continuing itstransport to downstream reachesmaximizes gravel use by "recycling"it over the years as it routes throughsuccessive storage sites (bars).Except for the reach under Old andNew Basso Bridges (RM 47.5), thecriteria used to identify bedloadimpedance reaches was (1) thepresence of a depositional lobe in alarger pool (Figure 3-1), (2)indications of immobile bed surface,and (3) downstream bed coarsening.At Old Basso Bridge, we measuredbedload transport during flows up to9,400 cfs and found no sedimenttransport of particles greater than 32mm. The local surface D 50rangedfrom 50 to 70 mm (visual estimate), and thecurrent high flow regime appears inadequate tomobilize the median grains of the bed surface inthis long, flat reach. In most of the bedloadimpedance reaches, no particles larger than coarsesand (

GEOMORPHIC AND RIPARIAN INVESTIGATIONSAll of the bedload impedance reaches in Table 3-1, with the exception of SRP 7 and 8, are encompassedin restoration project conceptual designs inChapter 4. If all these projects were implemented,the ability of the river to route bedload throughoutthe gravel-bedded reach would be restored ifsufficiently high flows are provided to mobilizecoarse bedload particles (gravels and cobbles).The discharge needed to mobilize the bed isdiscussed next.3.1.2. Bed mobility thresholds(Attribute #3)Bed mobilization is a fundamental process ingravel bedded rivers. Bed mobilization initiates avariety of alluvial functions, including bedloadtransport, transporting fine sediment fromspawning gravels, particle sorting of the bedmaterial, and spatial sorting of the coarse surfacelayer. In unimpaired alluvial stream channels, bedmobilization typically begins at or slightly lessthan bankfull discharge. Observing a threshold ofbed mobility is difficult because direct observationof the bed surface is usually not possible duringperiods of high flow and sediment transport.Therefore, we used two different methods toevaluate bed mobility: 1) tracer rock experimentsduring a high flow release from NDPP, and 2) bedmobility modeling at hydraulically simplereaches. Tracer rocks are usually painted aflorescent color so they can be easily located.Because it is not possible to observe exactly whenthe rocks moved, the tracer rocks were notintended to document an exact threshold discharge;rather, they document if the threshold hadbeen exceeded. If properly installed to accuratelyrepresent the adjoining bed particles, tracer rocksprovide the most accurate means of predictingmobility thresholds. In the absence of high flowsand/or time to wait for a high flow, bed mobilitymodeling can provide some reasonable thresholdestimates for hydraulically simple reaches. Tracer RocksAs this Restoration Plan was beginning in 1996,flood control releases provided a 5,400 cfs flow tomonitor bed mobilization with tracer rocks. Ourobjective was to evaluate whether 5,400 cfs wastransporting gravels and cobbles at varyinglocations within the gravel bedded reach (RM 25-52). Another objective was to determine thedischarge needed to mobilize the D 84particle inthe M.J. Ruddy Mitigation Project (a spawningriffle reconstructed in 1990). The D 84particlerepresents the framework of the alluvial streambed,so if the D 84is mobilized, we can safelyconclude that the "bed" is mobilized.Ideally, tracer rocks that represent the D 84sizeclass of the local bed surface would be placed onthe bed surface prior to a high flow. TuolumneRiver flows were already high when we beganwork on the fluvial geomorphic components ofthe Restoration Plan Therefore, we could not goto sample sites and collect particle size distributionsprior to the high flow release, nor couldtracer rocks be placed properly on the bed prior tothe high flow. We chose to use a compromisemethod of inserting several hundred tracer rocksbetween 25-150 mm prior to the 5,400 cfs release,but during the 3,600 cfs release (Table 3-2).Tracer rocks were either dropped off a bridge orthrown into the river, instead of traditional handplacement. By doing this, mobility potential wasgreater for these tracer rocks than native bedparticles because the tracer rocks are functionallyCHAPTER 3Table 3-2. Insertion location, quantity, and size range of tracer rocks on the Tuolumne River.Site River Mile Particle Size QuantityGeer Road Bridge (downstream side) 26.0 55-100 mm (2-4 inches) 375M.J. Ruddy Conveyor Bridge (upstream side) 36.2 50-150 mm (2-6 inches) 300M.J. Ruddy 4 Pumps Restoration Site 36.7 30-150 mm (1-6 inches) 300(riffle crest above the replaced riffle)Riffle 4B (left 1/3 of the channel) 48.5 55-100 mm (2-4 inches) 360New La Grange Bridge (upstream side) 49.9 25-150 mm (1-6 inches) 335Old La Grange Bridge (upstream side) 50.5 25-150 mm (1-6 inches) 25079

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 3Figure 3-2. Location of tracer rock experiments and bed mobility modeling in the gravel-bedded zone, Tuolumne River.in motion at the time they hit the streambed, andare more likely to be transported downstreamthan they would be "plucked" from the streambedduring natural conditions.Tracer rocks were inserted at six sites on 23March 1996 (Figure 3-2, Table 3-2). The dailyaverage discharge for the day was 4,300 cfs at theLa Grange gaging station.Immediately after our rock insertion, the flowincreased to 5,300 cfs for several days, thendropped to less than 3,000 cfs for several weeks.Experiments were left in place because higherflows were expected. On May 17th, 1996, flowspeaked at an instantaneous discharge of 6,880 cfs(Figure 3-3).In September, we attempted tracer rock recoveryat each site, and measured travel distances, if any.Of all the sample sites, the only location withsignificant transport distance was Riffle 4B (RM48.5). At two sites, M.J. Ruddy conveyor bridgeand Geer Road Bridge, the tracer rock experimentswere discarded. We did not attemptrecovery at the M.J. Ruddy conveyor bridgebecause upon noting the channel conditions at lowflow (300 cfs), we realized it was too deep torecover the tracer rocks and was also a poormodeling location. At the Geer Road Bridge, wewere unable to relocate any tracer rocks. We arenot sure what happened to the tracer rocks, butour bed mobility modeling indicates that the flowat this site did not approach the flow required tomove the rocks, and we are virtually certain thatthe rocks were not transported by the hydrographshown in Figure 3-3. The loss of these rocks isperhaps due to vandalism, or possibly by subsidenceand/or burial under sand.From these experiments, we concluded that thecoarse bed particles in most reaches in the gravelbeddedzone are not significantly mobilized byflows up to 6,880 cfs (Table 3-3). This result wassimilar to those observed from our bedloadtransport measurements taken at the Old BassoBridge (RM 47.4) [see next section]. This is notto say that the bed was static riverwide. Riffle 4Bmarked rock observations and visual observationat the M.J. Ruddy 4-pumps project (immediatelyupstream of the M.J. Ruddy Mitigation Project)suggest that 6,880 cfs is capable of mobilizingcobbles and gravels. Possible reasons for this80

GEOMORPHIC AND RIPARIAN INVESTIGATIONSuniqueness include: 1) the channel morphologywas reconstructed at both reaches to a smallerdimension better scaled to the post NDPP highflow regime, and 2) local gravel/cobble supplywas larger than adjacent reaches, allowing theriver to mobilize those gravels and cobbles. Thishas important implications for improving riverdynamics through channel reconstruction, gravelaugmentation, and high flow managementprescriptions. Bed mobility modelsBed mobility models were developed for five ofthe sites where tracer rock experiments wereconducted (M.J. Ruddy conveyor bridge site wasdiscarded). Models were calibrated and testedbased on our tracer rock observations. Theobjective of bed mobility modeling is to predicthydraulic conditions (and discharge) that causesincipient mobility of the bed surface. Models arealso used to evaluate whether a proposed channeldesign will facilitate bed surface particles to bemobilized during a bankfull discharge event(Attribute #3).Modeling cross section sites were selected withhydraulic characteristics that were easily quantifiedand modeled. Modeling required a variety offield data, including channel geometry obtainedfrom cross section surveys, high water stage anddischarge estimates, longitudinal water surfaceslopes during high flows, and bed surface particlesize distributions. With level surveys, we surveyedthe channel cross sections to an elevation aboveour expected high flow elevation and surveyedwater surface slopes through the reach during oneor more high flows. In some cases, we surveyedflood marks and debris lines instead of actualwater surface profiles. We quantified the particlesize distribution of the bed within our modelingreaches using modified Wolman pebble counts(Leopold 1970; Wolman 1954). Using the stage,discharge, and slope data, we back-calculatedManning's roughness coefficient (n) for eachsection.Armed with this hydraulic and particle size data,we applied a tractive force equation, shieldsequation, and Andrews (1994) bed mobilitymodel to predict the average depth needed tomobilize the D 84particle of the bed surface.CHAPTER 381

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR80007000Intended 5,400 cfs experimental releaseInstantaneous Peak Discharge 6,880 cfs on 5/17/96Discharge at La Grange (cfs)60005000400030002000Tracer Rock Insertion(Approx. 3,600 cfs)Tracer Rock Recovery1000CHAPTER 33/103/153/294/124/265/105/24Figure 3-3. Tuolumne River at La Grange streamflows during tracer rock experiments.Using calibrated Manning's roughness values, weapplied Mannings flow resistance equation topredict the discharge at that average depth.Further details of this method can be found inAndrews (1994).Results of bed mobility modeling suggested thatthe D 84would not be mobilized by flows less than7,000 to 8,000 cfs (Table 3-3). Our experiencecomparing tracer rocks with model results onsimilar gravel bedded rivers showed that D84Shields parameter of 0.020 to 0.025 causedmobility of the D 84particles (McBain & Trush1997). The modeling predictions tended tosupport our tracer rock results, but the next stepof predicting incipient motion was more problematic.Most modeling sites chosen were wheretracer rocks were inserted, and the hydraulics atthese locations did not approximate uniform flowas required for simple tractive force equations.This tended to make hydraulic predictions highlyvariable and less accurate. For example, flowsqueezing through bridges is accelerating underthe bridge, and decelerating upstream and6/76/217/57/198/21996 Day of Year8/168/309/139/2710/1110/2511/811/22downstream of the bridge. The simple equationsused in this analysis are not meant to be appliedunder these conditions. The best cross sections topredict incipient motion of the bed were the crosssections at the M.J. Ruddy 4-Pumps Restorationsite, because:• channel reconstruction attempted to size thechannel to the post-NDPP flow regime.• channel reconstruction removed much of theriparian vegetation that fossilizes many reachesof the Tuolumne River.• high flows from 1993-1996, combined with thecoarse sediment supply provided by the restorationactivities, allowed the channel to adjustitself.• hydraulics at most cross sections better approximateduniform flow conditions.This site also was attractive because previous highflows in 1993-1996 up to 8,500 cfs had causedthe channel to adjust, pools to develop, andchannel migration to occur. These dynamicchannel processes are desired for future restora-82

Table 3-3. Hydraulic characteristics of selected flows observed on the Tuolumne River in WY 1996 and 1997, with tracer rock results.RiverMileSiteCrossSectionDischarge(cfs)WaterSurfaceSlope (ft/ft)TotalWidth (ft)HydraulicRadius (ft)ShearStress(Pa)D84(mm)D84ShieldsParameterEffectiveWidth (ft)EffectiveHydraulicRadius (ft)EffectiveShearStress (Pa)EffectiveShieldsParameterMarkedRocksMobilized?50.5 Old LaGrange 0+29 5,410 0.00080 261 6.4 6.4 98 0.010 158 8.0 19.2 0.012 NoBridge 7,600* 0.00080 312 8.8 8.8 98 0.013 158 11.8 28.1 0.018 N/A8,700 0.00080 314 7.3 7.3 98 0.011 158 9.7 23.3 0.015 N/A60,000 0.00120 484 11.9 11.9 98 0.027 158 16.0 57.3 0.036 N/A49.9 New LaGrange 26+15 5,410 0.00104 311 3.2 10.0 148 0.004 126 5.1 15.9 0.007 NoBridge 8,700 0.00104 311 4.2 13.1 148 0.005 126 6.7 20.9 0.009 N/A60,000 0.00104 452 12.9 40.2 148 0.017 126 13.4 41.7 0.017 N/A8348.5 Riffle 4B 103+55 5,410 0.00133 514 3.0 12.0 124 0.006 149 5.2 20.7 0.010 Partial36.6- M.J. Ruddy 107+71 5,410 0.00095 205 4.5 12.7 N/A N/A 82 5.8 16.4 N/A N/A37.5 4 Pumps 99+14 5,410 0.00140 197 4.2 17.4 N/A N/A 120 4.8 20.1 N/A N/A94+97 5,410 0.00180 171 5.1 27.5 93 0.018 128 5.0 27.1 0.021 N/A88+10 5,410 0.00140 186 4.8 20.4 81 0.016 107 5.9 24.9 0.019 N/A79+61 5,410 0.00151 387 3.2 14.6 91 0.010 102 5.3 23.9 0.016 N/A67+53 5,410 0.00139 197 5.7 23.6 81 0.018 111 5.0 20.9 0.016 N/A60+61 5,410 0.00148 200 5.1 22.5 78 0.018 106 6.4 28.2 0.022 no26.0 Geer Road 0+84 4,000 0.00050 316 5.4 8.0 43 0.012 116 11.2 11.2 0.016 N/ABridge 6,880 no7,600 0.00043 400 9.6 12.4 43 0.018 116 11.7 15.0 0.022 N/A*conditions after 1/3/97 flood flood event event (60,000 (60,000 cfs peak), cfs peak), which which caused caused significant significant bed downcutting channel downcuttingCHAPTER 3GEOMORPHIC AND RIPARIAN INVESTIGATIONS

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 3tion efforts. Bed mobility modeling at crosssections 67+53, 88+10, and 94+97 (using a D 84Shields parameter of 0.022) predicted dischargesof 9,800 cfs, 7,050 cfs, and 8,250 cfs wouldmobilize the bed surface at this restoration site.The latter two cross sections (88+10 and 94+97)represent those that best approximate uniformflow conditions during high flows. Predictions atthese two cross sections should be weightedhigher than others. While these incipient flowpredictions indicated the bed is mobilized atapproximately 7,000 to 8,000 cfs, it is notimplied that wholesale bed scour occurs at thisflow. These data simply estimate a threshold forD 84mobility in the bed surface of riffles. Larger,short-duration discharges are still neededperiodically to cause bed scour below the surfacelayer to remove encroaching vegetation and torejuvenate alluvial features (see Section 3.2). Management implicationsBed particle mobility and transport are functionsof discharge, sediment size, sediment supply, andchannel morphology (channel dimensions andslope). The inability of the Tuolumne River tomobilize its bed particles during contemporaryhigh flow events is a result of reduced flowmagnitudes and more than 100 years of bedloadsupply loss and subsequent bed coarsening. Werecommend the following remediation:• Channel restoration projects should construct anarrower bankfull channel that conveys flowsbetween 4,000 cfs and 5,000 cfs and mobilizesthe D 84of the bed surface. Additionally, flowslarger than 5,000 cfs should begin to inundatethe floodplain and deposit fine sediments on thefloodplain. The floodplain should be sufficientlywide that flows of at least 15,000 cfs donot damage the bankfull channel. The relationshipbetween bankfull channel and bed mobilityis important: as flows approach bankfulldischarge, the bed particles begin moving, butas flow exceeds bankfull discharge, floodplainsbegin conveying flow and attenuate the rate ofincrease in water velocity and shear stresswithin the bankfull channel. This designreduces the risk of channel damage during largeflows, and encourages beneficial processessuch as fine sediment deposition, marginalbedload transport, and marginal channelmigration.• Increase the magnitude and variability of highflows during flood control releases (seeSection 3.2) to surpass bed mobility thresholdsin the restored channel.• Add large volumes of gravel and cobble(between 8 mm and 128 mm) to encouragebedload transport and deposition. Increasing thebedload supply of these size classes willdecrease median particle size, reduce bedcoarsening, create salmon habitat, and encouragethe channel to adjust its dimensions asneeded.In reaches where channel morphology has notbeen able to naturally adjust to the post-dam flowregime, the Restoration Plan recommends eitheractive restoration of the site by channel reconstruction,or passive restoration of the site byintroducing large volumes of gravel and routingthem downstream to allow the channel to selfadjust.The lack of channel morphology selfadjustment is only evident in the gravel beddedreach, and gravel introduction and channelrestoration should focus entirely in this reach.3.1.3. Bedload transportElimination of coarse sediment supply to theTuolumne River downstream of La Grange Damhas caused severe channel degradation byscouring he channelbed, banks and gravel barsduring high flows, but not redepositing thesefeatures because coarse sediment supply fromupstream sources is blocked by the NDPP. Aspredicted in Figure 2-13, this process has cumulativelycaused local bed degradation, more extensivebed coarsening, and loss of instream storageof alluvium (active gravel bars). Biota such assalmon and aquatic invertebrates depend onalluvial deposits for habitat; loss of this habitathas reduced the production potential of the river.A preferable management strategy to satisfyAttribute 3 (see Chapter 2) in a regulated systemas the Tuolumne River would be to artificiallyintroduce coarse sediment at a size class and rateequivalent to the transport capacity of the highflow regime. For example, if a 14-day flow of5,000 cfs transported 8,000 yd 3 of coarse sedimentfrom the spawning reaches immediately downstreamof La Grange Dam, gravel would beartificially replaced by introducing the appropriatevolume immediately downstream of the dam.84

GEOMORPHIC AND RIPARIAN INVESTIGATIONSKnowing the volume of sediment transported by aflow of given magnitude and duration requireseither a large number of cross sections to documentchange in storage, or a reasonable bedloadtransport rating curve. Other than sedimentationrates into La Grange Reservoir from 1893-1923,coarse sediment transport data is not available onthe Tuolumne River in which any empiricalbedload transport relationships could be developed.The January 1997 flood provided an excellentopportunity to measure sediment transport thatwas not anticipated during the development ofthis Restoration Plan. Bedload transport wassampled at two similar discharges: 8,450 cfs on1/17/97 and 8,200 cfs on 1/30/ Bedload SamplingSampling occurred from the downstream side ofthe Old Basso Bridge (RM 47.5) using a 6-inchsquare crane-deployed Helley-Smith bedloadsampler (Helley and Smith 1971). Two replicatesamples were collected at each sample locationalong the transect, spaced no more than 20 ftapart over a total effective channel width of 160feet. At each vertical, the sampler was lowered tothe bed surface, allowed to catch bedload intransport for 60 seconds, and then quickly raisedto the surface. The bedload sample for eachvertical was labeled and bagged for dry sieving inthe lab.Because we were interested in the coarserfractions of bedload transport for evaluatinggravel introduction rates, we did not sievematerial finer than 0.5 mm. The portion of thesample caught in the pan was simply classed asfiner than 0.5 mm and weighed. The remainingsample was sieved into standard size classes, withresults presented in two class sizes: (1) coarserthan 2 mm, and (2) coarser than 8 mm. These twosize classes were chosen because 8 mm wasassumed to be the smallest grain size preferablefor spawning gravel introduction, and 2 mm istypically the smallest grain size that travelspredominately as bedload rather than in suspension.The dry weight of each bedload samplecoarser than 8 mm and 2 mm was measured,divided by the time of sample (60 seconds) tocompute a unit transport rate for each vertical,and multiplied by the cell width of each verticalto compute a transport rate for each cell. All cellswere then summed to compute a total bedloadtransport rate for particles coarser than 8 mmand 2 mm.Immediately after the bedload samples werecollected, water surface elevations and slopeswere surveyed through the sampling cross sectionto estimate hydraulic properties of the flow. Allelevations were based on the USGS benchmark onthe southwest bridge abutment (elev=175.61 1929NGVD). We fitted a bedload transport ratingcurve to our two data points using Parker's (1979)model to extrapolate to higher discharges.Both samples at the Old Basso Bridge werenear incipient conditions for small gravels butnot larger gravels. This minimal graveltransport size is also reflected in the lowtransport rates (Table 3-4).The reach under the Old Basso Bridge is theupstream-most bedload impedance reach on thelower Tuolumne River. The low slope at the OldBasso Bridge measurement cross section discouragescoarse bedload transport until dischargesexceed 8,000 cfs. For example, only 3 percent ofthe sample material was coarser than 16 mm, andall particles were finer than 32 mm. While thesample location was convenient and the 1997flood opportunistic for sampling, the Old BassoBridge does not adequately represent gravelexport from the primary spawning reachesupstream because we hypothesize that theCHAPTER 3Table 3-4. Summary table of 1997 bedload transport measurements collected at the Old Basso Bridge (RM 47.5).Date Discharge Stage Slope Effective shear Bedload transport Bedload transport(cfs) (ft) (ft/ft) stress (Pa) > 8 mm (tons/day) > 2 mm (tons/day)1/4/97 60,000 169.48 0.0013 90.8 Not measured Not measured1/17/97 8,450 158.33 0.0005 18.3 39 tons 180 tons1/30/97 8,200 157.90 0.0005 17.6 30 tons 64 tons85

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 3upstream end of this bedload impedance reachtraps much of the larger gravels transported fromupstream reaches. Except for extremely largefloods such as the 1/4/97 flood, spawning gravelsizedparticles are probably not transportedthrough the reach. However, our tracer rockobservations at Riffle 4B upstream showed thatgravel and cobble do begin to mobilize at 6,800cfs. Riffle 4B is located in a long, straight,rectangular channel reach, such that futurebedload measurements and hydraulic calculationscould be reasonably made. Additionally, Riffle 4Bis immediately upstream of the bedload impedancereach that extends upstream from the OldBasso Bridge; therefore, coarse bedload passingthrough Riffle 4B better represents coarse bedloadexport from the primary spawning reach. Management implicationsA long-term spawning gravel re-introductionprogram is essential to improve spawning andrearing habitat in the gravel-bedded reaches belowLa Grange Dam. Large volumes of gravel introductionwill also allow attainment of Attribute #3(coarse sediment budget), which will encouragethe river to re-exhibit dynamic fluvial processesthat have been largely missing since the NDPPwas completed in 1971. Two reaches should beprioritized for artificial coarse sediment introduction:the reach from La Grange Dam to BassoBridge (RM 52.0-47.5) and the reach fromPeaslee Creek to Waterford (RM 45.5-34.2). Acoarse sediment (spawning gravel) managementprogram should be implemented as follows:1. Artificially introduce a large volume ofcoarse sediment (cobbles and gravels) torestore coarse sediment storage in the reachbetween LaGrange Dam and Basso Bridge.2. Establish a bedload transport measurementstation at the downstream end of the respectivegravel introduction reach (e.g., near riffle4B for the La Grange to Basso Bridge reach)to measure the rate of bedload export fromthe reach. Develop a bedload transport ratingcurve for particles greater than 8 mm toquantify the volume of bedload exportedduring high flows for each water year. Analternative method would be to install a largenumber of cross sections in a particular reachand use them to monitor the volume of coarsealluvial storage loss as it is transported out ofa particular reach.3. Annually introduce spawning gravel volumesequal to that exported by the previous winterhigh flows. For example, on June 1 of a givenyear, if 5,500 yd 3 of spawning gravel (greaterthan 8 mm diameter) was exported from thespawning reach below La Grange Dam fromOctober 1 to June 1, then 5,500 yd 3 would beintroduced that summer to replace graveltransported out of the reach. Gravels wouldbe inserted in the reach between La GrangeDam (RM 47.9) and Riffle 5B (RM 47.9).4. Monitor spawning gravel introduction byestablishing 10 to 15 cross sections inalluvial reaches between La Grange Dam(RM 52.0) and Basso Bridge (47.5) todocument alluvial deposit evolution (e.g.,determine if upstream gravel introduction isreplenishing alluvial features). If bedloadtransport measurements are not done, thenumber of cross sections would need to begreatly increased. Also, install tracer rocks tomeasure the downstream distance introducedgravel and cobble are transported each year.The intent of this method is for gravel introductionto keep pace with gravel export from thespawning reach during high flow events, tomaintain the coarse sediment budget (Attribute5), scour and redeposit alluvial materials (Attributes3 and 4), and maintains diverse chinooksalmon habitat (Attribute 1). Additionally,introducing clean spawning gravel will decreasethe percentage of fine sediment in these premiumspawning gravels, thus increasing egg-toemergencesuccess and increasing smolt productionin the river. Gravel introduction should befocused in the upstream reach first, due to itsimportance to salmon spawning and rearing. Wealso recommend adding gravel to reaches downstreamof Basso Bridge, but at the upstream endof reaches with bedload transport continuity (i.e.,reaches where bedload impedance has beenremoved through restoration, such as the upstreamend of the Gravel Mining Reach [Reach 5]).Measuring coarse bedload transport is difficultand expensive. Modeling is less expensive, butfraught with assumptions and inaccuracies thatcan render results unrealistic. If modeling ispursued, we recommend the approach developedby Wilcock (1997) that fits a bedload transportmodel to a small number of bedload measurements(usually less than 10). This provides thebenefits of economy and accuracy.86

GEOMORPHIC AND RIPARIAN INVESTIGATIONSSUSPENDED LOADBEDLOADDissolvedLoadWashLoadFine component ofBed Material LoadCoarse component ofBed Material LoadTOTAL SEDIMENT LOADProportions of total sediment load in each box is unique to each watershedFigure 3-4. Delineation of total sediment load generated from a given watershed. The coarse component of bedmaterial load is typically beneficial to salmon (e.g., spawning gravel, point bars), while the fine component of bedmaterial load is typically harmful to salmon (e.g., clogging of spawning gravels, embeddedness).Future bedload measurements should not becollected at the Old Basso Bridge, becausebedload transport of coarser size fractions doesnot occur through this reach at flows less than8,500 cfs. However, tracer rock experimentsshowed that mobility is beginning to occur atRiffle 4B at 5,400 cfs. We recommend installing aseasonal cableway immediately downstream ofRiffle 4B to collect bedload transport measurementsthat document spawning gravel exportrates. Five to ten bedload transport measurementsshould be collected each year, using a cataraft andcrane-deployed 6-inch Helley-Smith sampler tocollect samples. At the end of the high flowseason, a bedload transport rating curve should beprepared as described by Wilcock (1997) forparticles coarser than 8 mm, and using dischargerecords for the year at the La Grange gagingstation, compute annual spawning gravel exportvolumes annually. Because the reach immediatelydownstream of La Grange Dam has not hadsignificant coarse sediment supply since 1893, theimmediate need for a large quantity of gravel toreverse 100 years of sediment starvation exceedsthe need for annual replenishment. We recommendan initial "gravel transfusion," in which alarge volume of gravel (> 50,000 yd 3 ) is placed inthe channel throughout the reach to re-create thealluvial deposits eroded over the years. Thesedeposits would also be immediately functional asspawning habitat. Once this transfusion isimplemented and alluvial features recreated, theyearly gravel introduction program describedabove would maintain these features in thefuture. 4 More detailed methodology, proposedcoarse material introduction locations andvolumes, and estimated costs for implementationare provided in the "Tuolumne RiverSediment Management and ImplementationPlan" proposal, in Section Fine sediment sourcesFine sediment is frequently considered anindicator of degraded watersheds and instreamhabitat conditions, but it is also a normal componentof the total sediment yield from all watersheds.Simply defining "fine sediment" is problematicas there is little agreement on whichparticle size classes should be classified as finesediment. We use the 8 mm size class to definefine sediment for two reasons: 1) 8 mm is a lowerlimit for defining coarse sediment, which aretransported primarily as bedload; and 2) particlescoarser than 8 mm are generally beneficial tosalmon habitat, while particle size classes finerthan 8 mm are increasingly more deleterious tosalmon habitat as the proportion of fine sedimentincreases. Tappel and Bjornn (1983) relatedsurvival to emergence of chinook salmon andsteelhead to the percentage of particles finer that9.5 mm and 0.85 mm, and found that "survival ofchinook salmon embryos was more stronglyaffected by material from 0.85 mm to 9.5 mm indiameter."4The CA Department of Fish and Game began implementationof coarse sediment introduction in 1999, with placement ofapproximately 10,000 yd 3 of gravel to reconstruct riffle R1A,located immediately downstream of the Old La Grange Bridge.CHAPTER 387

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 3Fine sediment can be subdivided into the "fine bedmaterial load" (portion of fine sediment loadfound in the bed surface) and "washload" (theportion of fine sediment load not found in the bedsurface) (Figure 3-4). The former, typicallybetween 8 mm and 0.125 mm, is particularlyharmful to salmon habitat (e.g., spawning gravels).The latter is finer (typically silts), and on properlyfunctioning rivers usually only deposits onfloodplain surfaces that have lower velocities thanthe main channel. Washload sediment typicallyhas a low frequency of contact with the bedsurface within the active channel, and thustypically does not impact salmon habitat. Highconcentrations of washload may, however, havedeleterious effects on fry and juvenile chinooksalmon. Washload sediment deposits on floodplainsurfaces during floods, benefiting naturalriparian regeneration by creating moist seedbeds.Therefore, most effort to reduce fine sedimentshould focus on sources of fine bed material load(sands). To focus the following discussion, theterm "sand" will be used to represent this fine bedmaterial load. Additionally, sources of washloadshould be de-emphasize, as this component doesnot typically impair spawning habitat, does notappear to be excessively high on the TuolumneRiver, and can greatly improve riparian regenerationin areas where transport and depositionalprocesses are functional.Regarding fine sediment sources, our objectiveswere to:1. Identify point sources of sand causingsignificant habitat degradation (via largeinput rates and/or proximity to key salmonhabitat).2. Recommend specific remedial actions tocurtail these sand inputs into to theTuolumne River. Methods and resultsPoint sources were typically stream channels orlarge gullies. Non-point sources were usuallysheet erosion from orchards or fields and fluvialerosion of bank material. We focused on thestream channels and large gullies because theyconverted non-point sources in the watershed topoint sources inputting sand directly into theTuolumne River. Additionally, treatment of thesepoint sources is easier than treating non-pointsources. There are currently programs and effortsin place to address non-point sources of finesediment input, such as those programs currentlyunder the purview of the NRCS. We evaluated thegravel bedded reach between La Grange Dam(RM 52.0) and Waterford (RM 31.5) becausedownstream reaches are naturally transitioninginto the sand-bedded zone. The reach from LaGrange Dam to Lower Dominici Creek (RM 47.9)was further prioritized because a majority ofsalmon spawning occurs in this reach. Wecombined methods to evaluate the relativemagnitude of sand sources, with the followingmethodological progression:1. Evaluate topographic maps and soil maps tohypothesize significant sand contributorsbased on drainage area and soil type.2. Evaluate and compare tributary deltasobserved in 1993 aerial photographs, as thesephotos reflect over 6 years of drought (lowmainstem Tuolumne River flows should allowdeltas to accumulate).3. Field reconnaissance to evaluate potentialcontributors by identifying indicators ofrelative sand contribution (deltas, sandstorage in channel, sand plumes immediatelydownstream of tributaries) and assessingwhether sand is being delivered to theTuolumne River.Point sourcesThe primary factors affecting sand delivery to theTuolumne River by tributary channels and gulliesare watershed size, hydrology, stream channelslope, weathering products and erosivity ofunderlying soil types, and land use. Boundaries ofthe individual tributary watersheds were delineatedon USGS 1:24,000 scale quadrangles frombelow La Grange Dam (RM 52.0) to Waterford(RM 31.5), and tributaries were ranked bywatershed size to predict potential for sand input.The soil coverage contained within each of thedelineated watersheds was then evaluatedaccording to the USDA Soil Conservation ServiceSoil Coverage Maps (1964) to determine whichwatersheds contained soils most likely to deliversand to the Tuolumne River. All watersheds had alarge proportion of sandy loams, with lesseramounts of gravelly loams and meikle clays.Additionally, land use on the uplands outside theriver corridor was dominated by livestock grazing(nearer to La Grange) and orchards (near RobertsFerry). Land use along the river corridor was88

GEOMORPHIC AND RIPARIAN INVESTIGATIONSTable 3-5. Potential fine sediment point sources between RM 32 and RM 52.RM Bank Tributary Sand input potential51.3 North Mill gulch Low50.3 North Gasburg Creek Large49.7 North Morton Gulch Dissipates on floodplain/terrace48.9 North Upper Dominici Creek Dissipates on floodplain/terrace47.8 North Lower Dominici Creek Moderate47.0 North Un-named gulches at Basso Br Low45.5 North Un-named gulch Dissipates onto floodplain/terrace45.2 South Peaslee Creek Large44.7 North Rairden Gulch Dissipates onto floodplain/terrace41.0 North Salter Gulch Dissipates onto floodplain/terrace40.5 North Numerous gullies Dissipates onto floodplain/terrace40.2 North Warner Gulch Unknown, no delta observed39.5 North Roberts Ferry Nut Company gully Sediment excavated from roadside38.9 North Un-named gully Dissipates onto floodplain/terrace38.6 North Un-named gully Dissipates onto floodplain/terrace38.2 North Un-named gully Low (empties to Ketcham Slough)37.0 North Sidecast from orchard road Low (sheet erosion into river)35.5 North Un-named gully Dissipates onto floodplain/terrace35.3 North Road cut erosion Dissipates onto floodplain/terrace34 South Hickman Drain Low (long, flat backwater)CHAPTER 3primarily livestock grazing, row crops, or alfalfacultivation; however, because these areas werenearly flat (low slope), sand generation within thecorridor soils appeared to be very low.The June 8, 1993 aerial photographs capture theTuolumne River after a relatively wet water yearpreceded by five relatively dry water years. Peakdischarges at LaGrange were less than 2,000 cfsthroughout the five dry years and one wet wateryear. We hypothesize that the mainstem flowswere low enough for significant deltas wouldpersist. Therefore, any resultant tributary deltas inthe Tuolumne River visible in the June 8, 1993air photos could be used as a measure of therelative sediment loading by individual tributariesand gullies to the mainstem over five droughtyears and one wet year.Of all the tributaries upstream of Waterford (RM32.0), only three tributary deltas were conspicuousin the June 8, 1993 air photos: Gasburg Creek(RM 50.3), Lower Dominici Creek (RM 47.8),and Peaslee Creek (RM 45.2). Based on 1997field observations, we initially estimated averagetributary delta depths of 6 feet. Using thisapproximation, the approximate delta volumes forGasburg Creek was 380 yd 3 , Lower DominiciCreek was 325 yd 3 , and Peaslee Creek was 380yd 3 . By assuming a depth of 6 feet, volumeestimates are simply surrogates for surface area ofdelta material. This evaluation showed that thesethree tributaries were delivering enough finesediment to the Tuolumne River to be observed ona 1 inch = 500 ft scale aerial photograph. Noother tributaries had observable deltas.In April 1997, all tributaries and gullies within thestudy area were located and inspected to verify/refute observations from the 1993 aerial photographs,and to evaluate whether tributaries andgullies were delivering their sand load into theTuolumne River. Most gullies on the valley wallsempty onto cultivated fluvial terraces; thencultivation spreads the sediment and prevents it89

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 3from being delivered directly to the TuolumneRiver. Tributaries that deliver fine sediment directlyto the Tuolumne River are few (Table 3-5).To estimate particle size delivered by tributariesand gullies, bulk samples were collected ofdeposited material at a road cut gully at RM 35.3and at the Gasburg Creek delta at RM 50.3 (Table3-5). Sandy loam soils along the Tuolumne Rivercorridor, typical of the road cut gully sample, had100 percent of particles finer than 2 mm but only18 percent finer than 0.125 mm. Therefore, soilerosion from hillslopes is predominately sandsizedrather than silt-sized, indicating thathillslope and orchard erosion on uplands candeliver a large proportion of sand to the river. TheGasburg Creek delta sample was coarser, but alsohad a low percentage of the sample finer than0.125 mm. The D 50(median grain size) was 14mm, 35% of the sample was finer than 4 mm, andonly 1% of the sample was finer than 0.25 mm.The 1997 flood accessed the New Don PedroDam spillway for the first time in its history.Approximately 45,000 cfs flowed down TwinGulch, causing 25 to 50 feet of incision down tothe underlying bedrock, generating a tremendousvolume of coarse and fine sediment. Most coarsesediment was deposited in La Grange Reservoir;however, much of the sand was transportedthrough La Grange Reservoir and deposited in theTuolumne River channel downstream. Threetransects were surveyed through Twin Gulch toestimate the volume of topsoil washed downstream,mapping soil/bedrock contact lines andextrapolating this contact across the gulch. Weestimate over 200,000 yd 3 of topsoil alone wasexcavated and delivered to La Grange Reservoir,with much of these finer sediments transportedover the dam into the lower Tuolumne River. Thisfine sediment was primarily sand, which depositedonto floodplain surfaces downstream. Sanddeposition on the "floodplains" between LaGrange Dam and Basso Bridge (RM 47.5) was upto three feet deep (estimated average depth wasapproximately 0.5 feet).The Lower Dominici Creek delta and GasburgCreek delta were measured to estimate theportion of fine sediment delivered to theTuolumne River during the January 1997 floods.The existing tributary deltas were assumed to havedeposited on the receding limb of the flood.Recent deposition, approximating recedinghydrograph limb deposition, was approximately100 yd 3 for both Lower Dominici Creek andGasburg Creek. The Gasburg Creek tributary deltawas difficult to discern because the tributarysediment deposits were intermixed with sanddeposits from prior depositional events. Therefore,these values represented a minimum volumeof fine sediment delivery; the actual value isprobably much larger. For a rough yardstick, 100yd 3 is enough fine sediment to cover 325 linearfeet of the Tuolumne River low water channelsurface to a depth of 1 inch. Actual fine sedimentdelivery to the Tuolumne River was most likelymuch larger because the tributary floods precededthe large (60,000 cfs) spill into the TuolumneRiver, which most likely eroded much of any deltamaterial deposited in the preceding days.Rivers naturally sort much of their fine sedimentby deposition onto floodplains during high flows.However, in regulated rivers such as theTuolumne River, sand is often delivered to themainstem channel by tributaries when the mainstemis not flooding the floodplains. This sandaccumulates in the low water channel rather thanbeing deposited on the floodplain. Therefore,chinook salmon habitat is quickly degraded by inchannelsand deposition.Non-point sourcesNon-point sand sources are those that supply sandover an extended area, rather than from a singlepoint. The two primary non-point sand sourcesare bank erosion and sheet/surface erosion. Thenumber of these non-point sources along theTuolumne River upstream of Waterford (RM 32)are few. The natural banks along the TuolumneRiver are composed of a variety of sedimentclasses, ranging from clay hardpan to cobbles tosandy loam. Bank erosion is nearly non-existentin the study reach based on sequences of aerialphotographs and observations during our riverreconnaissance. Channel migration has notoccurred since New Don Pedro Dam was built,except near the 7/11 Materials plant site (RM37.8) and from eroding topsoil dikes throughoutthe gravel mining reach (RM 35.7 to 39.0). Theriver was migrating into a cultivated field at the 7/11 Materials plant site, and was rip-rapped in1997. This rip-rap eliminated this source of finesediment, but it also eliminated an importantsource of gravel, which supported extensivelyused spawning riffles immediately downstream.Bioengineering approaches should be used in thefuture in place of rip-rap if bank erosion must be90

GEOMORPHIC AND RIPARIAN INVESTIGATIONSeliminated at a certain location. The topsoil dikesthrough the rest of the reach continue to fail andcontribute fine sediment to the channel, butrestoration of a wider floodway throughout thisreach will eventually replace these dikes withfloodplains. The other significant source of finesediment is infrequent failure of dikes that isolatefine sediment settling ponds at gravel extractionsites. Failure of dikes separating these settlingponds from the bankfull channel results in largevolumes of fine sediment input into the river.Additional fine sediment is introduced by the dikefailure itself. This occurred at several locationsduring the 1997 flood and at least one location in1998. While much of this sediment is probablywashload, there is probably a significant volumeof sand-sized fine sediment delivered to theTuolumne River. The floodway restoration projectthrough the gravel mining reach will greatlyreduce future fine sediment inputs from thesesites. SummaryOf all the gullies and tributaries investigated,Gasburg Creek, Lower Dominici Creek, andPeaslee Creek are the primary sand contributors.Much of the sand originating from Gasburg Creekhas historically resulted from sheet runoff fromthe sand extraction operation immediately northof the Old La Grange Bridge. Gasburg Creek hasthe highest potential to negatively impact salmonhabitat because it delivers sand at the upstreamend of the most important reach for salmonproduction. Remediation for Gasburg Creek issimple; a sedimentation pond near its mouthwould prevent nearly all harmful fine sediments(between 0.1 mm and 8 mm) from entering theTuolumne River (see Sediment Management Plansummary in Chapter 4). Lower Dominici Creekand Peaslee Creek enter the Tuolumne Riverthrough incised channels; there is little spaceavailable near their mouths to construct a sedimentationpond. There may be some opportunityto construct a head control structure on LowerDominici Creek immediately upstream of theMID canal, but no site reconnaissance has beenconducted. Improved land use practices, particularlyalong tributary watercourses, could alsoreduce fine sediment inputs. We recommend spotHelley-Smith bedload measurements with a 3-inch sampler during storm runoff events to betterevaluate sand contribution from Lower DominiciCreek before proceeding with remediation.Constructing floodplains and increasing themagnitude and variability of high flow releaseswill help mitigate the negative impact of finesediment delivery from the watershed by encouragingnatural deposition on floodplain surfaces.During high flow releases, sediment finer than 1mm is typically transported in suspension in themainstem Tuolumne River; fluvial access tofloodplain surfaces will cause these sediments todeposit on the floodplains, reducing the proportiondepositing in the mainstem channel.3.1.5. M.J. Ruddy 4-Pumps restorationproject evaluationBetween 1992 and 1993, a restoration andmitigation project immediately upstream of theSanta Fe Aggregates (formerly M.J. Ruddy) plantsite (RM 36.7 to 37.6) was implemented toreconstruct nearly one mile of channel. Theunique feature of this project was that it attemptedto reconstruct an alluvial channel sized to thepost-dam flow regime, with bankfull channel,floodplains, and terraces. Past restoration activitiesprimarily focused on modifying the activechannel (mostly riffle rehabilitation) and plantingriparian vegetation. In the summer of 1991, theM.J. Ruddy Mitigation Project reconstructedsouth bank dikes to increase floodway capacity to11,000 cfs from RM 36.7 to 37.0, and to providefloodplain and terrace surfaces through this reach.In the summer of 1993, the San Joaquin Districtof the California Department of Water Resources(DWR) implemented the M.J. Ruddy 4-PumpsChannel Restoration Project. This project constructeda new bankfull channel geometry andplanform from RM 36.7 to 37.6, and constructedfloodplain and terrace surfaces from RM 37.0 to37.6. The most significant component of theproject was moving the bankfull channel approximately200 feet north from RM 37.3 to RM 37.6to reduce erosion into an orchard, and redistributingsteep drops in channel elevation back into lowgradient pool-riffle sequences to improve chinooksalmon habitat.From the end of construction in 1993 to thebeginning of 1997, several high flow eventsoccurred, ranging from 5,000 cfs to 9,000 cfs,which were large enough to cause the channel toadjust its bed and bank morphology. These highflows provided a unique opportunity to evaluatehow a reconstructed, appropriately-scaled channelwould respond to high flow events. Would theCHAPTER 391

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 3channel adjust and create new pools and riffles?Would the channel migrate and increasesinuosity? Monitoring would also provideinformation on as-built channel roughness values(Manning's n) to apply to other restoration projectdesigns, and to evaluate changes in reach-wideroughness as riparian vegetation matures andchannel planform evolves.A shortcoming of the M.J. Ruddy 4-PumpsProject was that as-built surveys were not conducted,so quantitative comparisons could not bemade. Anecdotal descriptions from DWR wererelied upon instead. Cross sections, thalwegprofiles, and water surface profiles for 250 cfs and5,410 cfs were surveyed (Figure 3-5). Crosssections (Figures 3-6 to 3-12) were surveyed inthe 4-Pumps reach only. After cross sectionswere input into HEC-RAS, roughness values wereadjusted until the predicted 5,410 water surfaceprofile matched the profile measured in the field(Figure 3-13). This calibration discharge wasappropriate because flows between 4,500 cfs and5,500 cfs have been typically used as a desiredfuture design bankfull discharge. Manning's nvalues at 5,410 cfs ranged from 0.027 to 0.029,significantly lower than typical values used byengineers in more vegetated channels (0.035).We expect that over time roughness values willbegin to approach 0.035. This evolution inroughness should be incorporated into futurechannel designs by designing floodplain surfacesbased on 5,500 cfs and Manning's n value of0.028, which will result in lower floodplains thanif Manning's n is 0.035. As vegetation maturesand roughness increases, floodplains may beginnaturally aggrade from fine sediment deposition.Particle size was documented with modifiedWolman surface pebble counts (Leopold 1970) atmany of the cross sections, to evaluate bedmobility thresholds and track changes in particlesize over time (Table 3-6, which includes particlesize data from other sites). Results of bed mobilitymodeling are discussed in Section 3.1.2. The asbuiltsinuosity and longitudinal pool-riffletopography was of particular importance, becauseour interest was in observing the evolution ofpools, riffles, and planform geometry. Aerialphotographs taken in June 1993 capture theproject being constructed, showing a very slightsinuosity. As-built topographic expression ofpools was between 1 and 2 feet (K. Falkenberry-DWR, personal communication). Wet water yearsin 1995 and 1996 caused several flood controlreleases of sufficient magnitude to initiate bedmobility (Table 3-7). In the summer of 1996, the4-Pumps reach had evolved considerably duringthe high flows of 1995 and 1996, so we surveyedcross sections and thalweg profiles to inferchanges (Figure 3-14). No planform evaluationwas performed, other than noting that the outsidesof many meanders were actively eroding andsinuosity was increasing. Due in part fromchannel migration, point bar building on theinsides of bends was evident (Figures 3-7, 3-10,3-11, 3-12). The thalweg profile through the 4-Pumps reach showed a regular pool-riffleTable 3-6. Particle size distribution summary for Tuolumne River pebble counts collected in summer 1996.River CrossMile Section Location* Morphology D84 D5050.5 0+21 STN 118-203 Run, center of channel 98 mm 58 mm49.9 26+15 STN 14-140 Riffle, center of channel 148 mm 100 mm48.5 103+55 Not recorded Riffle, center of channel 124 mm 86 mm36.7 60+61 STN 26-132 Riffle, center of channel 78 mm 45 mm36.8 67+53 STN 52-62 Upper point bar 58 mm 30 mmSTN 62-75 Point bar 56 mm 22 mmSTN 75-195 Run, center of channel 81 mm 52 mm37.0 79+61 STN 63-143, 300-367 Pool/run, left bank point bar & right side of channel 64 mm 36 mmSTN 143-300 Pool/run, left side of channel 91 mm 62 mm37.2 88+10 STN 38-180 Pool, center of channel 81 mm 50 mm37.3 94+97 STN 17-72 Riffle w/median bar, right bank channel 70 mm 40 mmSTN 79-169 Riffle w/median bar, left bank channel 93 mm 48 mm26.0 0+94 STN 63-98 Riffle, center of channel 43 mm 25 mm* Stationing is in feet from left bank cross section pin92

GEOMORPHIC AND RIPARIAN INVESTIGATIONSTable 3-7. Water years 1995 to 1997 flood histories at the Tuolumne River at La Grangegaging station.WATER YEAR 1995January 30-February 17March 18-19March 25-31April 1-23May 4-June 6July 10-12WATER YEAR 1996February 7-March 28May 17-22WATER YEAR 1997December 13-21January 3January 11-March 3DISCHARGE4,000 cfs to 5,070 cfs8,200 cfs8,000 cfs to 8,300 cfs6,800 cfs to 8,300 cfs7,600 cfs to 8,700 cfs (peak=9,260 cfs)8,000 cfs to 8,600 cfs4,500 cfs to 5,500 cfs6,700 cfs (peak=6,880 cfs)5,500 cfs to 5,800 cfs51,000 cfs (peak=60,000 cfs)7,000 cfs to 9,000 cfssequence developing, with ½ wavelengths ofapproximately 1,000 ft and pool depths of 3 to 4ft (Figure 3-14). These meander wavelengthsmatch well with predicted values in the literature,and will be useful for designing future restorationprojects.Because the 1997 flood (60,000 cfs) was muchlarger than the design floodway through thisreach (11,000 cfs), dikes failed at RM 38.5, 37.6,37.1, 36.6, and 35.7-36.2. The large magnitude ofthe 1997 flood, combined with these local dikefailures, caused areas of large bed scour anddeposition. In general, bed scour occurred wherethe river was confined (e.g., RM 37.1 to 37.6).Bed deposition occurred where dikes failed,causing a rapid decrease in sediment transportcapacity (e.g., RM 37.0). The process that causesthis is vital, as it highlights the importance offunctional floodplains and adequate floodwaycapacity in maintaining channel morphology andsalmon habitat.3.1.6. Channel design considerationsAs mentioned briefly, the 1997 flood causedsignificant damage to the M.J. Ruddy 4-Pumpsproject. This damage was not just limited to theM.J. Ruddy reach, nor was it limited to 60,000 cfsfloods. Dikes in mining reaches commonly failedduring flows exceeding 8,000 cfs. Most problemsduring high flow events are caused by insufficientfloodway capacity from aggregate extractiondikes, agricultural encroachment, and riparianencroachment. A classical two stage channel,containing a bankfull channel that conveys mostcoarse sediment, and a floodplain channel thatconveys much of flood flows, provides a dynamicchannel and a stable channel (Figure 3-15). Therate of bedload transport is a function of shearstress; the larger the shear stress, the larger thepotential for channel damage. The two phasedchannel provides enough shear stress to transportbedload at marginal rates, but floodplain inundationreduces the rate of increase in shear stress,thereby reducing the risk of significant channeldamage. The key is to design the bankfull channelto transport bedload, and design the floodplainwidth and elevation such that the floodwayconveys large discharges without abnormallylarge velocities and shear stresses.This importance of a properly sized two-stagechannel is best illustrated by an example from theTrinity River. Shear stress distributions measuredon a reach of the Trinity River confined byriparian encroachment, and a reach of the TrinityRiver where the riparian berm was removed andfloodplain re-established. In the confined channel,an increase in discharge from 3,000 cfs to 6,500CHAPTER 393


GEOMORPHIC AND RIPARIAN INVESTIGATIONScfs doubles maximum shear stress, and themaximum shear stress remains concentrated inthe center of the channel (Figure 3-16). Incontrast, in the restored reach, an increase indischarge from 2,500 cfs to 5,100 cfs decreasesmaximum shear stress slightly, and moves thezone of maximum shear stress onto a point barsurface (Figure 3-17). In the former case,concentrating high shear stress in the center ofthe channel during large flood events causessignificant channel downcutting, whereas shiftingshear stress (and therefore scour) onto the pointbar surface performs the desired function ofpreventing riparian encroachment along the lowflow channel. Many confined reaches of theTuolumne River were degraded by the 1997 floodby significant downcutting. Cross sections at theOld La Grange Bridge and New La Grange Bridgedocument several feet of downcutting (Figures 3-18 and 3-19); other reaches, such as within theM.J. Ruddy 4-Pumps Restoration Project (Figure3-20), downstream of Roberts Ferry Bridge, andother confined reaches also responded bydowncutting. This scoured material was transporteddownstream until the confinement ended,either by a break in riparian vegetation, valleyexpansion, or dike failure. In several locations,entire riffles were scoured out (Figure 3-20).The link between these fluvial processes andsalmon habitat can easily be illustrated: 1)channel downcutting in the confined reachremoves spawning riffles and bars that providerearing habitat, 2) scoured material depositsdownstream, raising the riffle crest elevation,creating a long backwater upstream and a verysteep riffle downstream (Figure 3-21). Not onlyis habitat lost by scouring, but deposition increasesriffle slope to the point where velocitiesexceed suitable ranges and reduce habitat. This ispartially illustrated at the M.J. Ruddy 4-PumpsRestoration Project, where Riffle 34A was scouredaway (Figure 3-20). Therefore, the key to creatingand maintaining a healthy Tuolumne Riverchannel and associated habitat is to increasefloodway capacity, and (re)construct properlysized two-stage channels that convey flow andcoarse sediment, but also safely convey largefloods of at least 15,000 cfs. A vegetated floodway500 feet wide in the gravel bedded reachesshould safely convey 15,000 cfs and provideenough room for some channel migration.Increasing the floodway capacity will alsoincrease the ability of the flood managementsystem to better avoid extreme floods as experiencedin 1997. Additionally, increasing flows inthe 8,000 cfs to 15,000 cfs range will greatlybenefit the Tuolumne River channel and habitat bymobilizing the bed surface, transporting finesediment, discouraging future riparian encroachment,and allowing the channel to adjust itsdimensions if necessary. The opportunity toincrease the frequency of high flows in the 8,000cfs to 15,000 cfs range in a way that avoidsimpacts to water supply and minimizes impacts topower generation is evaluated in the followingsection.3.2. FLOOD FLOW EVALUATIONFloods are natural events within river corridors.Floods are also negatively perceived by the public.However, as scientific understanding of riverecosystem function has developed, it has becomeapparent that floods are actually crucial to ahealthy river ecosystem. As discussed in Chapter2, floods are responsible for attaining severalAttributes of Alluvial River Integrity. While somerestoration programs acknowledge the need forrestoring floods (e.g., flushing flows, channelmaintenance flows), recommending and implementingmanaged high flows have been limited.The 1996 flood release on the Colorado Riverfrom Glen Canyon Dam is perhaps the mostnoteworthy. Several recommendations areprovided for improving Tuolumne River floodrelease management that could greatly aid inrehabilitating and maintaining dynamic riverinehabitats. These recommendations are based onquantifying thresholds for important fluvialprocesses (e.g., bed mobility, bedload transportrates, gravel introduction rates).3.2.1. Fluvial geomorphic thresholdsRecalling that frequent bed surface mobilizationis a fundamental attribute of healthy alluvialrivers (Attribute No. 3), an important restorationobjective is to improve the ability of the river tomobilize its bed surface. The term "general bedmobility" is used to describe mobilization of theD84 size class over most portions of the channelbed.Bed mobilization typically occurs in naturallyfunctioning alluvial rivers at, or slightly lessthan, bankfull discharge (Andrews 1983, Leopold1994). Bankfull discharge typically rangesCHAPTER 395

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR110Left bank looking downstreamRight bank105Elevation (ft)10095Pond10/30/96 Ground surface10/30/96 Water surface (Q=355 cfs)903/29/96 Water surface (Q=5,400 cfs)5/18/96 Water surface (Q=6,900 cfs)10/31/96 pond water surface85-100 -50 0 50 100 150 200 250 300 350 400 450CHAPTER 3Distance from Left Bank Pin (ft)Figure 3-6. M.J. Ruddy mitigation site, cross section 60+61.110Left bank looking downstreamRight bank9/6/96 Ground surface9/6/96 Water surface (Q=285 cfs)1053/29/96 Water surface (Q=5,410 cfs)Elevation (ft)1009590-100 -50 0 50 100 150 200 250 300 350 400 450Figure 3-7. M.J. Ruddy 4 Pumps site, cross section 67+53.Distance from Left Bank Pin (ft)96

GEOMORPHIC AND RIPARIAN INVESTIGATIONS110105Left bank looking downstreamRight bank9-6-96 Ground surface9/6/96 Water surface (Q=285cfs)3/29/96 Water surface (Q=5,410cfs)Elevation (ft)1009590-100 -50 0 50 100 150 200 250 300 350 400 450Distance from Left Bank Pin (ft)Figure 3-8. M. J. Ruddy 4 Pumps site, cross section 79+61.110Left bank looking downstreamRight bankCHAPTER 3105Elevation (ft)100959-6-96 Ground surface9/6/96 Water surface (Q=285cfs)3/29/96 Water surface (Q=5,410cfs)90-100 -50 0 50 100 150 200 250 300 350 400 450Figure 3-9. M. J. Ruddy 4 Pumps site, cross section 88+10.Distance from Left Bank Pin (ft)97

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR110Left bank looking downstreamRight bank105Elevation (ft)100959/11/96 Ground surface9/11/96 Water surface (Q=285cfs)3/29/96 Water surface (Q=5,410cfs)90-100 -50 0 50 100 150 200 250 300 350 400 450CHAPTER 3Distance from Left Bank Pin (ft)Figure 3-10. M. J. Ruddy 4 Pumps site, cross section 94+97.110Left bank looking downstreamRight bank105Elevation (ft)100959/11/96 ground surface9/11/96 Water surface (Q=285cfs)3/29/96 Water surface (Q=5,410cfs)90-100 -50 0 50 100 150 200 250 300 350 400 450Distance from Left Bank Pin (ft)Figure 3-11. M. J. Ruddy 4 Pumps site, cross section 99+14.98

GEOMORPHIC AND RIPARIAN INVESTIGATIONS110Left bank looking downstreamRight bank105Elevation (ft)1009/11/96 ground surface959/11/96 water surface (Q=284 cfs)3/29/96 Water surface (Q=5,410 cfs)90-100 -50 0 50 100 150 200 250 300 350 400 450Figure 3-12. M. J. Ruddy 4 Pumps site, cross section 107+71.1101059/4/96 Thalweg profile9/4/96 Water surface profile (Q=250 cfs)5,400 cfs Water surface elevationDistance from Left Bank Pin (ft)Santa Fe Aggregatesconveyor bridgeSanta Fe Aggregateshaul road bridgeCHAPTER 3Elevation (ft)10095Reed haulroad bridge9085806,0005,0004,0003,0002,0001,0000-1,000-2,000-3,000-4,000-5,000-6,000-7,000-8,000-9,000-10,000-11,000-12,000Warner/Dierdorffproperty lineFigure 3-7 to 3-13cross sectionsDistance from (RM 35.6) Warner/Deardorff property line (ft)Figure 3-13. Tuolumne River 1996 longitudinal profiles from river mile 34.6 to 37.8 (Section 24 and 32 T.3S., R.12E.).99

CHAPTER 3100Elevation (ft)110105100959085M.J. Ruddy HaulRoad BridgeXS 60+61 XS 67+53 XS 79+61 XS 88+10 XS 94+97 XS 99+14 XS 107+71Pre-constructionPoolsDevelopingPoolDevelopingPoolDevelopingPoolDevelopingPool9/4/96 Water surface profile (Q=250 cfs)9/4/96 Thalweg profile5,400 cfs Water surface elevationPre-constructioPoolTUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR80-5,000-5,500-6,000-6,500-7,000-7,500-8,000-8,500-9,000-9,500-10,000-10,500-11,000Distance from (RM 35.6) Warner/Deardorff Property Line (ft)Figure 3-14. Thalweg and water surface profiles through the M. J. Ruddy 4-Pumps restoration site, river mile 36.8 to 37.7 (Section 29 and 30 T.3S., R.12 E.).

GEOMORPHIC AND RIPARIAN INVESTIGATIONSElevation (ft)(A)185180175170165Bedload transport beginsBankfull channelFloodwayFloodplainLarge flood, but moderate shear stressFlow exceeds bankfull, lowering rate ofincreasing shear stress lowers as flowsaccess floodplain-50 0 50 100 150 200 250 300 350 400 450 500Elevation (ft)(B)185180175170165FloodplainBankfull channelFloodwayLarge flood, extremely high shear stress incenter of channelFlow exceeds bankfull, shear stress continues toincrease due to confinementBedload transport begins slightly below bankfull discharge-50 0 50 100 150 200 250 300 350 400 450 500CHAPTER 3Elevation (ft)(B)185180175170165FloodplainBankfull channelFloodwayLarge flood, extremely high shear stress incenter of channelFlow exceeds bankfull, shear stress continues toincrease due to confinementBedload transport begins slightly below bankfull discharge-50 0 50 100 150 200 250 300 350 400 450 500Figure 3-15. Natural two-stage channel (A), and impact of encroached (riparian, urban, agricultural, and/oraggregate extraction) channel, (B) and unconfined channel, and (C) on shear stress and bedload transport.101

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORRelative elevation (ft)876543210-1-2-3-4-5-6-7-8-9-10-11Left bank looking downstreamRiparian bermRight bank6/92 ground surface6,500 cfs water surface3,000 cfs water surface3,000 cfs shear stress field6,500 cfs shear stress fieldRiparianberm-12-400 20 40 60 80 100 120 140 160 180 2006050403020100-10-20-30Shear stress (Pascals)CHAPTER 3Distance (ft)Figure 3-16. Shear stress distribution on Trinity River cross sections confined by riparian encroachment.Relative elevation (ft)11010910810710610510410310210110099989796Left bank looking downstreamRight bank956/96 Ground surface945,100 cfs water surface elevation -20931,850 cfs water surface elevation5,100 cfs shear stress field924,000 cfs shear stress field -30912,500 cfs shear stress field901,850 cfs shear stress field-400 20 40 60 80 100 120 140 160 180 2006050403020100-10Shear Stress (Pascals)Distance (ft)Figure 3-17. Shear stress distribution on Trinity River cross sections in unconfined restored reaches.102

195190185Elevation (ft)180175103170165160-100 -50 0 50 100 150 200 250 300 350 400 450Distance from Left Bank Pin (ft)Figure 3-18. Cross section at Old La Grange Bridge (RM 50.5) showing channel downcutting resulting from January 1997 flood (60,000 cfs).CHAPTER 310/31/96 Ground surface6/30/97 Ground surface3/29/96 Water surface (5,400 cfs)10/31/96 Water surface (300 cfs)1/3/97 Water surface (60,000 cfs)1/28/97 Water surface (8,500 cfs)Base of Old La Grange BridgeGEOMORPHIC AND RIPARIAN INVESTIGATIONS

CHAPTER 3104Elevation (ft)19519018518017517016516010-31-96 Ground surface6-30-97 Ground surface1995 HWM (8,710 cfs)3/29/96 Water surface (5,410 cfs)10/31/96 Water surface (400 cfs)1/3/97 Water surface (60,000 cfs)6/30/97 Water surface (300 cfs)Bottom of New LaGrange Bridge-50 0 50 100 150 200 250 300 350 400 450TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORDistance from Left Bank Pin (ft)Figure 3-19. Cross section at New La Grange Birdge (RM 49.9) showing channel downcutting resulting form January 1997 flood (60,000 cfs).

GEOMORPHIC AND RIPARIAN INVESTIGATIONS1009896Gravel DepositionRiffle 35ARiffle 34A94Elevation (ft)929088Riffle 36ARiffle 35BXS 2093+00Scour from 1997 FloodXS 2123+00XS 2129+008684Relic InstreamGravel Mining Pit9/4/96 Thalweg Profile10/28/99 Thalweg Profile82MJ Ruddy Haul Road Bridge80207,000 208,000 209,000 210,000 211,000 212,000 213,000Longitudinal Stationing from Tuolumne River mouth (ft)Figure 3-20. Longitudinal profiles of Tuolumne River downstream of Old Basso Bridge before and after theJanuary 1997 flood (60,000 cfs), illustrating scour and loss of riffles due to channel confinement.CHAPTER 3between the 1.5 to 2.5-year recurrence flood onan annual maximum flood frequency curve. Thisrelationship allows us to initially estimate a bedmobilization discharge based solely on a floodfrequency curve. The bankfull discharge alsoapproximates the discharge class responsible forchannel sizing, so any change in bankfull dischargewill change the ability of the river to formand maintain its channel. The 1.5-year recurrenceflood at the La Grange gaging station (RM 51.6)decreased from 8,600 cfs to 3,000 cfs as a resultof the New Don Pedro Project (NDPP). For thepost-NDPP 1.5-year flood to continue mobilizingthe bed surface, channel size (cross sectionalarea) and/or particle size must decrease commensuratewith the reduction in the channel formingflood. Bed mobility experiments, bed mobilitymodeling, and bedload transport samplingindicates that flows in excess of 7,000 cfs to8,000 cfs are presently required to begin generalmobilization of the bed surface. This thresholdbed mobilization discharge is much larger thanthe post-dam 1.5 to 2.5 year flood for tworeasons: (1) the present channel is a relic of thepre-NDPP channel morphology, scaled to thelarger pre-NDPP high flow regime, and (2) thebed has most likely coarsened due to coarsesediment deficit, raising the flow thresholdnecessary to mobilize the bed particles. Properlysizing future channel restoration projects andartificially restoring coarse sediment supply byintroducing large volumes of coarse sediment(between 8 mm and 128 mm), should provide amore natural frequency of bed mobilization.Another important threshold is the discharge thatbegins to inundate contemporary floodplains.Unfortunately, the reduction in flows, extensivechannel disturbance, and low sediment supplyhave prevented any distinct post-NDPP floodplainsto form, so this threshold could not beevaluated.Other thresholds, such as bed scour and channelmigration, were not quantified during this study.Observations at the M.J. Ruddy 4-Pumps projectduring 1995-96 showed that slow channelmigration was occurring during flows ranging105

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 3Figure 3-21. Conceptual evolution of pool-riffle morphology in confined reaches of the Tuolumne River.106

GEOMORPHIC AND RIPARIAN INVESTIGATIONSfrom 5,400 cfs to 8,500 cfs; however, because asbuilt(post-construction) conditions were notsurveyed, the channel migration rate could not bequantified.3.2.2. Feasibility of using floodmanagement or power peakingreleases to improve fluvialprocessesA healthy river has both high flows and low flows(Attribute 2). Sustained steady summer baseflowsencourage riparian initiation. Without subsequenthigh flows, this vegetation will mature andfossilize the channel as observed on the StanislausRiver, Trinity River, Clear Creek, upper SacramentoRiver, and others. A range of floodmagnitudes provides varying degrees of fluvialprocesses, exceeds important geomorphic thresholds,and creates diverse, high quality salmonhabitat. While post-NDPP flood control releaseson the Tuolumne River have helped minimize thedegree of riparian encroachment and channelfossilization compared to other regulated riverswithin the Central Valley region, fluvial processesand habitat within the Tuolumne River couldgreatly benefit by increasing the magnitude andfrequency of high flows. One important opportunityto improve the magnitude and frequency ofTuolumne River high flows is to incorporategeomorphic objectives in flood control releases.Moderate-to-high flows on the Tuolumne Riverare periodically released for three purposes: lowmagnitude (

CHAPTER 3108Table 3-8. Wy 1970-1997 instream releases, and potential modifications to peak flows to improve geomorphic processes.Rank ofMaximum Number of Number of Instream instream Recommended Duration Additional waterdaily average days flows days flows release release additional of peak volume bypassingWater Year discharge (cfs) >3,000 cfs >5,500 cfs (Acre-ft) volume peak flow (cfs) flow (days) power plant (Acre-ft)*1970 7,000 20 13 729,000 9 8,000 3 22,0001971 2,490 0 0 346,000 01972 1,450 0 0 164,000 01973 1,370 0 0 165,000 01974 1,940 0 0 376,000 01975 3,080 2 0 561,000 01976 2,730 0 0 360,000 01977 224 0 0 67,000 01978 4,570 10 0 292,000 5,500 3 01979 3,650 36 0 657,000 10 5,500 3 01980 7,280 76 38 1,493,000 5 10,000 2 44,0001981 2,980 0 0 441,000 01982 8,150 113 49 1,718,000 4 10,000 2 44,0001983 10,400 288 118 3,465,000 1 12,000 1 69,0001984 8,010 130 14 1,376,000 6 10,000 2 44,0001985 2,820 0 0 376,000 01986 6,870 68 37 1,134,000 8 10,000 2 44,0001987 2,980 0 0 283,000 01988 588 0 0 78,000 01989 767 0 0 61,000 01990 861 0 0 85,000 01991 1,190 0 0 83,000 01992 1,150 0 0 81,000 01993 1,760 0 0 241,000 01994 3,080 1 0 187,000 01995 8,710 151 89 2,185,000 2 12,000 1 69,0001996 6,790 77 9 1,183,000 7 8,000 3 22,0001997 55,865 96 74 1,959,000 3 12,000 1 69,000TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR*assumes flows exceeding 5,500 cfs bypass power house, ascending hydrograph limb is 2,000 cfs/day, and receding hydrograph limb is 1,000 cfs/day.Also assumes that canals are not in operation at the time of release, so that streamflows equal New Don Pedro Dam release.

GEOMORPHIC AND RIPARIAN INVESTIGATIONS• If possible, extend the duration of flows in the5,500 cfs range for several days after the peakflow event to transport fine sediment downstreamand deposit onto contemporary floodplains(designed to inundate at 4,000 cfs to5,000 cfs).• Larger releases (e.g., 12,000 cfs) should be ofprogressively shorter duration due minimizecoarse sediment transport capacity and attenuatehigh flow peak magnitudes in downstreamurban areas. Initial suggestions for high flowduration for 8,000 cfs, 10,000 cfs, and 12,000cfs fluvial geomorphic releases are 3-day, 2-day,and 1-day duration respectively to minimizedownstream gravel flux while exceeding bedmobility thresholds (Figures 3-22 to 3-29).• Down-ramping rates should be at, or lower than,rates specified in the FSA and ACOE floodcontrol manual to minimize juvenile chinooksalmon stranding.• Years in which flood management releases arenecessary tend to come in multi-year sequences;therefore, in the first wet year after severalsequential dryer years, a larger flow should bereleased if feasible (e.g., 12,000 cfs) to reverseriparian seedling initiation on active channelalluvial deposits, reducing riparian encroachmentrisk.• The magnitude and duration of these flowsshould be re-evaluated continuously as part ofthe adaptive management program to evaluatewhether bed mobility, bedload transport, sandtransport, channel migration, and bed scourobjectives are being met.• Extremely wet years with extensive floodcontrol releases in the spring should target verygradual ramping rates to encourage riparianregeneration on contemporary floodplains.Ramping rates targeting natural Fremontcottonwood regeneration should be less than 3cm/day to allow their taproots to follow thedescending moist capillary fringe.These recommendations were developed to avoidinterference with water allocations contained inthe FERC Settlement Agreement, and to minimizeloss of power generation revenues whenbypass flows would normally occur. We suggestthat geomorphic and biological monitoringexperiments be developed and implemented (e.g.,impacts of flow magnitude and duration to reddscour and egg mortality) prior to each winterseason, in the event flood management releasesoccur. We recommend that the TRTAC closelymonitor whether flood flows are achieving fluvialgeomorphic and biological restoration objectives.The most significant potential shortcoming of theabove approach is long sequences of dryer years(1971-1977, 1987-1994) that allow riparianvegetation to initiate and establish on newlyrehabilitated reaches and newly deposited alluvialsurfaces.3.2.3. Constraints (sediment supply,floodway width, structuralencroachment)One result of the January 3, 1997 flood peak wasthe immediate perception that we needed to dosomething to prevent this from happening again.Some commonly suggested immediate solutionshave been more storage (more or bigger dams),levees, or purchasing more flood control space inexisting reservoirs. Out of this reactionary noiseemerged a solution that could benefit a variety ofneeds: increased floodway capacity to improveflood management and flood control flexibility.There are several primary considerations whenconsidering flood management solutions: maintainagricultural and municipal water supplies,providing flood control, protecting private andpublic property, ensuring human safety, positiveand negative impacts to the environment, andcost. Purchasing flood control space in NDPPprovides additional flood control protection, butreduces water supply, imposes a large cost to thepublic, and reduces environmental benefitsprovided by higher flood control releases.Constructing levees can contain floods, but theyoften provide a false-protection by allowingdevelopment behind them, and when they fail,flood damage increases. Additionally, the cost oflevee construction and maintenance is large andgreatly reduces the environmental quality of theriver corridor.A logical, long-term solution is to restore acontinuous floodway and meander corridor fromLa Grange downstream to the San Joaquin Riverthat provides flood conveyance up to 15,000 cfsupstream of Dry Creek and 20,000 cfs to the SanJoaquin River. This strategy is integral to restoringfluvial geomorphic processes to the TuolumneRiver, while at the same time reducing the risk ofcatastrophic floods (e.g., 1997 flood), greatlyimproves salmon habitat, provides property andhuman protection, preserves agricultural andmunicipal water supplies, and provides operatorsCHAPTER 3109

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR15,00014,00013,00012,0001970, release at La Grange1970, w/ improved geomorphic flowsDaily Average Discharge (cfs)11,00010,0009,0008,0007,0006,0005,0004,0003,0002,0001,000CHAPTER 301-Oct 1-Nov 1-Dec 1-Jan 1-Feb 1-Mar 1-Apr 1-May 1-Jun 1-Jul 1-Aug 1-SepDate of YearFigure 3-22. Tuolumne River annual hydrograph for 1970 with hypothetical flood control release hydrographmodifications to improve geomorphic processes.15,00014,00013,0001980, release at La Grange1980, w/ improved geomorphic flows12,000Daily Average Discharge (cfs)11,00010,0009,0008,0007,0006,0005,0004,0003,0002,0001,00001-Oct 1-Nov 1-Dec 1-Jan 1-Feb 1-Mar 1-Apr 1-May 1-Jun 1-Jul 1-Aug 1-SepDate of YearFigure 3-23. Tuolumne River annual hydrograph for 1980 with hypothetical flood control release hydrographmodifications to improve geomorphic processes.110

GEOMORPHIC AND RIPARIAN INVESTIGATIONS15,00014,00013,0001982, release at La Grange1982, w/ improved geomorphic flows12,000Daily Average Discharge (cfs)11,00010,0009,0008,0007,0006,0005,0004,0003,0002,0001,00001-Oct 1-Nov 1-Dec 1-Jan 1-Feb 1-Mar 1-Apr 1-May 1-Jun 1-Jul 1-Aug 1-SepDate of YearFigure 3-24. Tuolumne River annual hydrograph for 1982 with hypothetical flood control release hydrographmodifications to improve geomorphic processes.15,00014,00013,0001983, release at La Grange1983, w/ improved geomorphic flowsCHAPTER 312,000Daily Average Discharge (cfs)11,00010,0009,0008,0007,0006,0005,0004,0003,0002,0001,00001-Oct 1-Nov 1-Dec 1-Jan 1-Feb 1-Mar 1-Apr 1-May 1-Jun 1-Jul 1-Aug 1-SepDate of YearFigure 3-25. Tuolumne River annual hydrograph for 1983 with hypothetical flood control release hydrographmodifications to improve geomorphic processes.111

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR15,00014,00013,0001984, released at La Grange1984, w/ improved geomorphic flows12,000Daily Average Discharge (cfs)11,00010,0009,0008,0007,0006,0005,0004,0003,0002,0001,000CHAPTER 301-Oct 1-Nov 1-Dec 1-Jan 1-Feb 1-Mar 1-Apr 1-May 1-Jun 1-Jul 1-Aug 1-SepDate of YearFigure 3-26. Tuolumne River annual hydrograph for 1984 with hypothetical flood control release hydrographmodifications to improve geomorphic processes.15,00014,00013,0001986, released at La Grange1986, w/ improved geomorphic flows12,000Daily Average Discharge (cfs)11,00010,0009,0008,0007,0006,0005,0004,0003,0002,0001,00001-Oct 1-Nov 1-Dec 1-Jan 1-Feb 1-Mar 1-Apr 1-May 1-Jun 1-Jul 1-Aug 1-SepDate of YearFigure 3-27. Tuolumne River annual hydrograph for 1986 with hypothetical flood control release hydrographmodifications to improve geomorphic processes.112

GEOMORPHIC AND RIPARIAN INVESTIGATIONS15,00014,00013,0001995, released at La Grange1995, w/ improved geomorphic flows12,000Daily Average Discharge (cfs)11,00010,0009,0008,0007,0006,0005,0004,0003,0002,0001,00001-Oct 1-Nov 1-Dec 1-Jan 1-Feb 1-Mar 1-Apr 1-May 1-Jun 1-Jul 1-Aug 1-SepDate of YearFigure 3-28. Tuolumne River annual hydrograph for 1995 with hypothetical flood control release hydrographmodifications to improve geomorphic processes.15,00014,00013,00012,0001996, released at La Grange1996, w/ improved geomorphic flowsCHAPTER 3Daily Average Discharge (cfs)11,00010,0009,0008,0007,0006,0005,0004,0003,0002,0001,00001-Oct 1-Nov 1-Dec 1-Jan 1-Feb 1-Mar 1-Apr 1-May 1-Jun 1-Jul 1-Aug 1-SepDate of YearFigure 3-29. Tuolumne River annual hydrograph for 1996 with hypothetical flood control release hydrographmodifications to improve geomorphic processes.113

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 3greater flexibility during flood managementreleases. Increasing the magnitude and variabilityof high flows will allow greater frequency ofexceeding thresholds for achieving Attributes(e.g., bed mobility, floodplain formation), whilereducing the risk of catastrophic floods.Constraints to increasing floodway capacity from9,000 cfs to at least 15,000 cfs are: 1) thin topsoildikes that confine the floodway through theGravel Mining Reach (RM 34 to 40) are presentlyinadequate, and 2) the Modesto sewage treatmentplant would require additional protection. TheGravel Mining Reach Restoration Project is beingimplemented to remove Constraint 1). The City ofModesto sewage treatment plant is presentlybeing upgraded to withstand floods up to 20,000cfs, and when completed, will remove Constraint2). In the Gravel Mining Reach, greater floodwaywidth will reduce future flood damage to activegravel mining operations.In the aftermath of the 1997 flood event, manylandowners in the lower river sought floodway orriparian easements to provide financial relief forrepeated flooding of their agricultural lands. Thiseasement program has recently added the 140acre Grayson River Ranch Project (RM 5-6). TheWetlands Reserve Program (administered by theUSDA Natural Resources Conservation Service incooperation with the East Stanislaus ResourceConservation District) and the Anadromous FishRestoration Program (USFWS) have funded andadministered the conservation easement agreementand riparian restoration program to date.Several other additional applications to thisprogram are pending easement funding.Other potential constraints include gravel lossimmediately downstream of La Grange Dam(which will require artificial introduction tocompensate), power generation losses duringflows exceeding the 5,400 cfs turbine capacity,and flood routing management in the entire SanJoaquin River floodway. However, the recommendedshort duration, large magnitude peakflows will minimize impacts to these constraints.These flows will transport and scour alluvialdeposits, but the short duration will minimize nettransport, thus minimizing gravel/cobble introductionneeds. The short duration peak will alsoreduce power generation losses and minimizeflood routing problems in the lower San JoaquinRiver. Because these flows exceed bed mobilitythresholds, and may exceed bed scour andchannel migration thresholds, they are fundamentalcomponents of this Restoration Plan. Insummary, increasing high flow release magnitude,combined with the improved floodwaywidth, should benefit salmon production as wellas improving flood management on the TuolumneRiver. These benefits can be extended to the SanJoaquin River, if improvements to floodway widthand similar actions occur there as well.3.3. AGGREGATE SOURCEINVENTORYThe aggregate source inventory summarizes thelocation and rough volumes of aggregate potentiallyavailable for restoration projects. Bydocumenting the volume and location of sources,overlaying property ownership, and computinghaul distances from source to restoration site, weevaluated the most cost-effective aggregatesources available. The inventory is based on ourown field reconnaissance and investigations bythe California State Department of Conservation,Division of Mines and Geology, in Special Report173 (Higgins and Dupras 1993). The geographicscope of Special Report 173 was specificallyconfined to Stanislaus County. The TuolumneRiver has a limited supply of aggregate comparedto the Merced River because the river bottomlandwidth is much narrower. Therefore, we revisitedpotential aggregate sources on the TuolumneRiver as well as those on the Merced River.Aggregate sources on these two rivers typicallyoccur in dredger tailings and "pit run" aggregateexcavated from historic terraces across the rivercorridor. Dredger tailings have had most of thegold removed and are commercially less valuablebecause organic material is often mixed with theaggregate. Pit run aggregate is much morecommercially valuable because it typically hasminor amounts of woody debris mixed in.Dredger tailings are therefore preferable restorationmaterials because they are in less demand bythe aggregate industry, and their use results inless conflict with preferred aggregate sources.3.3.1. Special Report 173Aggregate mineral resources in the County areclassified as (Higgins and Dupras, 1993):114

GEOMORPHIC AND RIPARIAN INVESTIGATIONS• Aggregate Resources, which include reservesas well as all potentially useable aggregatematerials that may be mined in the future, butfor which no mining permit has been granted,or for which marketability has not beenestablished.• Aggregate Reserves, which are aggregateresources determined to be acceptable forcommercial use, that exist within propertiesowned or leased by aggregate producingcompanies, and for which permits have beengranted to allow mining and processing.Special Report 173 identifies 540 million tons ofaggregate resources available in the StanislausCounty, of which 217 million tons are locatedwithin the Tuolumne River Geographic Area(Figure 3-30). Presently, permitted reserves total27.7 million tons for Stanislaus County, whichwill continue to increase over time as urbanexpansion and aggregate demand grows. Thereport identifies nearly the entire Tuolumne Rivervalley as an aggregate resource, and delineatespolygons within the valley (with estimatedaggregate depths) to estimate aggregate volumes;however, the polygon areas are too large to be ofuse in quantifying local gravel sources. Allestimated volumes assume that the aggregate isextracted to the maximum depth possible (bedrock),which ranges from five to thirty-five feet.This will result in additional pits adjacent to theTuolumne River, and increased confinement ofthe bankfull channel. We re-evaluated aggregatesources based on smaller, more site-specificpolygons, and in most reaches estimated aggregatevolumes based on excavating down to acontemporary floodplain elevation rather than tobedrock.3.3.2. McBain & Trush inventoryOur reconnaissance level survey focused ondredger tailings on the Merced River corridor,remaining dredger tailings in the Tuolumne Rivercorridor, and remnant materials left after dredgertailings were removed for construction of NDPP.The Merced River corridor near Snelling is nearly1.5 miles wide, three times wider than theTuolumne River corridor (0.5 miles wide). Theentire corridor width was dredged for gold in bothrivers, and the larger corridor width on theMerced River resulted in considerably moretailings. Additionally, slow growth in MercedCounty has reduced local aggregate demand, somost of the tailings remain. In contrast, rapidgrowth in Stanislaus County has created a largedemand for local sources of aggregate, andTuolumne River aggregate resources have beenrapidly dwindling. Demand on Merced Riversources will certainly rise as the new University ofCalifornia campus is constructed in Merced.A potentially competing use for aggregateresources will be river restoration; however, thereare some differences in aggregate quality needsbetween commercial and restoration uses.Because the channel restoration projects needinglarge volumes of aggregate are largely pit fillingprojects, woody material in the dredger tailings isirrelevant. Therefore, restoration efforts shouldtarget dredger tailings as the primary source ofconstruction aggregates, which could minimizefuture conflict or competition with commercialaggregate operators on the river.Because SMARA and Special Report 173consider dredger tailings to be part of the Countyaggregate resources, the use of dredger tailingsfor restoration projects would involve the entireCounty-use permit process, including CEQA anddevelopment of reclamation plans. Developmentof County use permits is time-intensive, andrestoration could leave considerable volumes ofaggregate left in place at restoration sites asmining pits are restored and instream gravelstorage is increased.We located potential aggregate sources on theTuolumne River and Merced River by searchingin the field. We classified a source as viable if itsatisfied the following criteria:• It was lower commercial quality than pit-runaggregate, so we would not be removing a highquality aggregate reserve from commercial/infrastructure use.• It could be extracted without creating a pit thatcould be connected to the river in the nearfuture to avoid perpetuating additional gravelmining pits adjacent to the river.• It could be extracted and the extraction siterestored to better conditions (creating shallowoff-channel wetlands, or restoring a functionalfloodplain connected to the river, or replacing axeric surface with native woody riparianvegetation).• It was within 20 miles one-way from most ofthe channel restoration projects planned for theTuolumne River.CHAPTER 3115

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 3Figure 3-30. California Division of Mines and Geology (CDMG) Aggregate Resource Areas (Higgins and Dupras1993) and currently permitted aggregate mining areas identified on the Tuolumne River between Santa Fe Bridge (RM21.7) and La Grange Dam (RM 52).Sites were given a higher priority if they were onpublic land, within the boundary of permittedaggregate extraction operation on dredgertailings, or on private land whose owners expressedan interested in having aggregate removedfrom their property. Priority was also giveto sites with large volumes within a single parcel,making permitting and other implementationconsiderations easier. Lower priority was given tosites on private land where the landowner hadeither not been contacted, or had not expressed aninterest in removing material. Our searchboundary on the Tuolumne River was from LaGrange Dam (RM 52.0) to Roberts Ferry (RM40); on the Merced River, it focused strictly ondredger tailings from Merced Falls (RM 55) tobelow Snelling (RM 45).Volumes for each site were estimated using simplemethods to provide reasonable accuracy with lowcost. We delineated the surficial extent of eachparticular deposit on orthorectified aerial photographsor topographic maps, then estimated thedepth of excavation for each boundary. Depthswere estimated by measuring the elevationdifference between the top of the deposit and areclamation surface elevation. The area of thedeposit multiplied by the depth of excavationprovided a volume estimate. There were a fewsites where aggregate operators provided volumeestimates, another site where topographicalsurveys provided volume estimates, and a fewsites where depths were not measured and novolumes were estimated. The locations andvolume estimates were digitized as a GIS layer tooverlay on assessors maps and to be able toestimate travel distance to future restorationproject sites.Results of our Tuolumne River surveys andMerced River surveys are shown on the Figures3-31 and 3-32, respectively, and in Table 3-9.Eight sites stand out among all the others: 1)Materials deposited into La Grange Reservoirduring the 1997 flood, 2) Reeves spawninggravels near La Grange (RM 50.5), 3) La GrangeReservoir delta, 4) Crooker dredger tailings(leased by Santa Fe Aggregates at RM 41), 5)Cree dredger tailings (leased by Western Stone atRM 42), 6) Hall dredger tailings at RM 43, 7)Zanker dredger tailings at RM 46, and 8) theMerced River Ranch (318 acres of Merced Riverdredger tailings) currently being purchased byCDFG. The Reeves spawning gravels are one of116

GEOMORPHIC AND RIPARIAN INVESTIGATIONSthe most important gravel resources left on theTuolumne River. The Reeves property is locatedon the north side of the Tuolumne River, and is anactive sand mining pit. A unique aspect of thissand deposit is that it is interspersed with thinlenses of small to medium gravels. As the sandhas been mined, the gravels were screened andstockpiled as waste material. There may be up to75,000 yd 3 of these gravels surrounding the sandpit. The range of gravel sizes contained in thesepiles is consistent with the range of gravel sizespreferred by salmon for spawning habitat.Because these gravels are stockpiles only severalhundred feet from the primary spawning area,introducing this gravel would be extremelyeconomical. Introducing large quantities of thismaterial back into the river is perhaps the highestrestoration priority for the Tuolumne River (seeSediment Management and Implementation Plandescription in Section 4.5.6)The La Grange Reservoir delta was formed duringthe 1997 flood, when 45,000 cfs was spilleddown Twin Gulch, incising a 25 ft to 50 ft gorgeinto the bedrock and depositing this material intoLa Grange Reservoir. Topographical surveysestimate near 500,000 yd 3 of fractured rock andsand available for removal at no purchase cost.This material should only be used to fill pitsbecause it is too angular for use as riverbedmaterial; using this material instead of aggregatewould reduce real and perceived loss of futureaggregate sources for societal use. The primarydrawback to using this material is the costassociated with constructing a road into thecanyon, trucking material out of the canyon, andtransporting it to downstream restoration sites.The Crooker Site is much closer to restorationsites, and contains large volumes of dredgertailings that are permitted for extraction. Closeproximity makes it an less expensive source.Santa Fe Aggregates estimates approximately4,000,000 to 8,000,000 tons (2,600,000 to5,200,000 yd 3 ) of material available if excavatedbelow groundwater in a manner similar todownstream pits. Creating new pits at this site,however, would create the same problem thematerial is being used to fix: in-channel and offchannelpits. Excavating down to a contemporaryfloodplain elevation would reduce the availablevolume to roughly one-half to one-third theestimated volume presented above. Because thesetailings are leased by a commercial aggregateCHAPTER 3117

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 3figure 3-31 Gravel inventory sites identified on the Tuolumne River between Roberts Ferry (RM 40) and La Grange Dam (RM 52)118

119Figure 3-32 Gravel inventory sites identified in the Merced River dredger tailings, near Snelling CA. Volumes estimated by Area*Depth/2 to provide more conservativevolume estimate in these variable height dredger tailings.CHAPTER 3GEOMORPHIC AND RIPARIAN INVESTIGATIONS

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORTable 3-9. Summary of upper Tuolumne and Merced River aggregate source inventory.CHAPTER 3TOULUMNE RIVER AGGREGATE SOURCESSite #ApproximateAverage Depth (ft.)Surface Area ofSource (sq ft)Surface Area ofSource (ac)Approximate Volumeof Source (cu. yd.)1 25 25,000 0.57 12,000 *2 Volume from DTM 20,000 0.46 2,0003 30 102,000 2.34 57,000 *4 27 5,000 0.11 3,000 *5 Volume from DTM 18,000 0.41 2,0006 10 87,000 2.00 32,0007 8 30,000 0.69 9,0008 2 22,000 0.51 2,0009 10 175,000 4.02 65,00010 12 16,000 0.37 7,00011 12 349,000 8.01 155,00012 20 101,000 2.32 75,00013 12 68,000 1.56 30,00014 5 159,000 3.65 29,00015 4 3,811,000 87.49 565,00016 2 592,000 13.59 44,00017 8 77,000 1.77 23,00018 3 1,647,000 37.81 183,00019 5 7,000 0.16 1,00020 3 143,000 3.28 16,00021 2 294,000 6.75 22,00022 1.5 252,000 5.79 14,00023 3 391,000 8.98 43,00024 3 11,000 0.25 1,00025 7 31,000 0.71 8,00026 2 375,000 8.61 28,00027 10 321,000 7.37 59,000 *28 15 126,000 2.89 35,000 *29 1 145,000 3.33 5,00030 15 46,000 1.06 26,00031 16 78,000 1.79 46,00032 3 182,000 4.18 20,00033 2.5 74,000 1.70 7,00034 1 122,000 2.80 5,00035 2.5 60,000 1.38 6,00036 10 282,000 6.47 104,00037 10 227,000 5.21 84,00038 10 295,000 6.77 109,000TOTAL: 1,861,000MERCED RIVER AGGREGATE SOURCESSite #ApproximateAverage Depth (ft.)Surface Area ofSource (sq. ft.)Surface Area ofSource (ac)Approximate Volumeof Source (cu. yd.)1 6.9 1,345,000 30.88 172,000 *2 6.9 1,434,000 32.92 183,000 *3 7.8 901,000 20.68 130,000 *4 7.8 1,778,000 40.82 257,000 *5 5.8 424,000 9.73 46,000 *6 10 2,496,000 57.30 462,000 *7 6.9 2,812,000 64.55 359,000 *8 4.3 1,224,000 28.10 97,000 *9 12 393,000 9.02 87,000 *10 11.5 8,687,000 199.43 1,850,000 *TOTAL: 3,644,000* These sources are undisturbed dredger tailings or gravel cones with "sawtooth" morphology.Volumes estimated by Area*Depth/2 to provide more conservative volume estimate in thesevariable height dredger tailings.120

GEOMORPHIC AND RIPARIAN INVESTIGATIONScompany, any negotiated change to the approvedreclamation plan would need to consider compensatingforgone mineral rightsThe Cree dredger tailings (RM 42) are also closerto restoration sites, but do not contain nearly thevolume of dredger tailings as the Crooker site andHall site. Most tailings were removed duringNDPP construction, and remaining tailings arecurrently permitted for extraction and leased by acommercial aggregate company. The Creedredger tailings (sites 33-38 on Figure 3-31) mayyield over 300,000 yd 3 of aggregate. The sitecould yield more aggregate volume if off-channelwetlands are created on the far north side of thefloodway (away from the bankfull channel). Verylittle volume remains in sources closer to theriver, and should not be excavated below acontemporary floodplain elevation (approximately4-5 ft above the low water surface) to avoidadditional pit capturing and salmon strandingproblems.The Hall dredger tailings (RM 43-44) have notbeen permitted or disturbed, and the landownerhas expressed interest in using these dredgertailings for local restoration purposes (Sites 18-32in Figure 3-31) (see Dredger Tailing Reachrestoration project in Section 4.3.8). Up to500,000 yd 3 are available if dredger tailings arelowered to contemporary floodplain elevation(approximately 4-5 ft above low water surface).We recommend these materials be used locally toimplement the Dredger Tailing Reach restorationproject because no on-highway hauling would beneeded and the available material should besufficient to restore SRP 2, SRP 3, recreatebankfull confinement, and add much neededgravel supply to the Tuolumne River.The Zanker dredger tailings (RM 46) were largelyremoved during NDPP construction; however,some areas still contain considerable quantities ofaggregate. The landowner has expressed interestedin using these remnant tailings for streamrestoration. The site is on the south side of LakeRoad (Sites 15 and 16 in Figure 3-31), isolatedfrom the Tuolumne River floodway. There isconsiderable topographic diversity on the site,with cottonwoods established in lower elevationsections (closer to the summer groundwatertable), and annual grasses and exposed cobblesover the remainder. There is tremendous opportunityto improve site conditions and increasewetland habitat with riparian vegetation. Theremay be over 600,000 yd 3 of material in this reach.The proximity of the aggregate source to potentialspawning gravel introduction sites, coupledwith potential landowner interest in restoring thesite, makes it a high priority aggregate source site.Finally, the Merced River Ranch, if CDFGcompletes their land purchase, could providenearly 2,000,000 yd 3 of aggregate for futurerestoration purposes (Figure 3-32). The primarylimitation for Tuolumne River use is hauldistance: 32 miles round trip to La Grange, 58miles round trip to Waterford, and 66 miles roundtrip to Geer Road Bridge over the TuolumneRiver.The sites with single landowner and largeaggregate volume should be used for largerrestoration projects. Numerous smaller sourcesidentified in Figure 3-31 and 3-32 should be usedfor smaller restoration projects, or when largelocal restoration projects could use them to reducetransportation and purchase costs. However, ifthese smaller sites are not permitted and SMARAcompliant, the effort expended to permit thesesmaller sites may cost more than if using alreadypermitted commercial sources. Therefore, eachrestoration project will need to evaluate sourcematerial on a case-by-case basis to determine themost cost-effective way of securing restorationmaterials.3.3.3. SummaryThere is a finite volume of aggregate within theTuolumne River; Higgins and Dupras (1993)estimatd that the volume of currently permittedreserves would be depleted by 2002 based onforecasted population growth for the region. Thelimited supply of commercial grade aggregate onthe Tuolumne River will increase the competitionfor these resources among aggregate operators aswell as restoration practitioners. To avoid thisconflict, we may be forced to use Merced Riverdredger tailings in restoration activities, whichmay significantly increase the cost and environmentalimpacts of future projects. To implementfuture restoration projects, the TRTAC must:1. Increase dialog with the aggregate extractionoperators to minimize future competition andconflict.2. Secure important dredger tailing deposits forfuture restoration projects, particularly thoseclosest to the river channel.CHAPTER 3121

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 33. Participate in future aggregate extractionpermitting to ensure that permitting conditionsaddress ecological, channel, andfloodplain conditions along the TuolumneRiver corridor. As in recently funded projectsto restore damage caused by previousaggregate extraction, preservation of sitesprior to resource development may be a lessexpensive alternative to restoration.3.4. RIPARIAN CORRIDOREVALUATIONSDramatic losses in riparian vegetation coverage,and the growing awareness that riparian vegetationis vital to river ecosystem integrity, haveelevated the importance of riparian vegetationpreservation and restoration. While benefits ofriparian vegetation to the river ecosystem andsalmon habitat have been well documented (Junket al. 1989; Stanford et al. 1996), interactionsbetween riparian vegetation and fluvial processeshave not.Our riparian evaluation had three components: 1)a detailed inventory of riparian vegetation alongthe lower 52 miles of the Tuolumne River, 2) adescription of current riparian vegetation bygeomorphic zone and reach, 3) an evaluation offluvial and hydrologic interrelationships withriparian vegetation in three channel morphologies,and 4) a discussion of factors limitingnatural regeneration. Improved riparian revegetationplans and channel/floodplain restorationdesigns will profit from these study componentsand will help identify and prioritize potentialriparian restoration projects (see Chapter 4).3.4.1. Tuolumne River RiparianInventoryThe first step in our riparian inventory of thelower 52 miles of the Tuolumne River corridorwas to choose a classification scheme for definingriparian vegetation units. We chose to use theplant series classification, developed by Sawyerand Keeler-Wolf (1995) because it incorporatesboth canopy dominance and subdominant understoryin the classification. The second step was tomap and inventory riparian vegetation boundariesbased on these plant series found in the TuolumneRiver corridor. Riparian Series ListA plant series is a vegetation sub-unit or standdominated by a single plant species, or sharedamong a few co-dominant species. Usually severalplants are associated with a series, though insome cases a series can be only one species (e.g.,Giant Reed Series). Sawyer and Keeler-Wolf(1995) define hundreds of plant series, 22 ofwhich were documented in the lower TuolumneRiver corridor (Appendix B). During the riparianinventory, we documented four new plant series:box elder, Oregon ash, tree of heaven, and ediblefig. Box elder and Oregon ash are native to theTuolumne River; tree of heaven and edible fig areexotic. Exotic plants are numerous, and comprisefive of the 29 observed series: eucalyptus, ediblefig, giant reed, lamb's quarters, and tree ofheaven.While most riparian vegetation fit into the Sawyerand Keeler-Wolf classification, some riparianvegetation could not be classified as a series.These deviations were typically a single plant(e.g., an isolated valley oak), or a small clump ofidentical individuals (e.g., weeping willow,Himalayan berry). These were mapped as individualplants, and labeled on the inventory mapsby including their scientific names in the maplegend (Appendix B) 5 .Of the 29 series identified, several have beengreatly reduced over time, making their perpetualexistence threatened, or very threatened. Theseseries often provide habitat for rare, threatened orendangered animal species. The Nature Conservancycharacterized the relative abundance ofCalifornia's general vegetation types (initiallycreated by Holland (1986)) using the CaliforniaDepartment of Fish and Game's Natural DiversityDatabase (NDDB) program. A series type isidentified as "threatened" if there is only 2,000 to10,000 acres of the remaining vegetation type leftin California.We included The Nature Conservancy classificationand the NDDB classification to match serieson the Tuolumne River with threatened vegetationtypes (Appendix B). All native terrestrialvegetation within the Tuolumne River riparian5A single riparian inventory map of the entire corridoris included in the back of the report. The complete setof 19 riparian inventory maps is included on theenclosed CD-ROM.122

GEOMORPHIC AND RIPARIAN INVESTIGATIONScorridor, with the exception of narrow-leafwillow and white alder, are classified as verythreatened or threatened (Appendix B). Riparian Species ListA list of common plant species in the lowerTuolumne River corridor was prepared (AppendixB). Each species was characterized by: (1) nativeor exotic, (2) whether the plant is invasive whenit colonizes a site (3) growth habits (tree, shrub,vine, etc.), (4) USFWS hydric codes (wetlandobligate, facilitative wetland plant, etc.), and (5)SCS codes. Of the 106 species comprising riparianvegetation inventoried, 64 were native and 42 wereexotic. Of the 42 exotic species observed, 26 wereinvasive and actively displacing native species.Native riparian plant species are adapted toflooding, channel migration, channel avulsion,and sediment deposition and scour that occurredbefore human alteration. Exotic plants have outcompetedmany native riparian plant species sinceflow regulation began because exotic plants arebetter adapted to the altered, post-NDPP ripariancorridor. Exotic plants are effective inter-specificcompetitors, often growing in pure stands thatexclude all other plant species. Many exotic plantspecies cover so much area within the ripariancorridor they were mapped as plant series. Fourexotic plant species represent 67% of all mappedexotic plants in the Tuolumne River ripariancorridor (Appendix B). Eucalyptus, edible fig,giant reed, and tree of heaven form large standsthat interfere with native hardwood recruitmentand regeneration. Stands of exotic species are soextensive and aggressive they greatly impairpotential riparian corridor recovery and should betargeted for removal in all future restorationprojects.Eucalyptus provides a good example of howexotic plants can alter an environment at theexpense of native species. Eucalyptus is plantedfor wind breaks and green strips due to its fastgrowth rate; however, its reproductive propensityhas allowed it to escape from urban plantings andinvade the riparian corridor. Eucalyptus has thelargest exotic species coverage in the ripariancorridor (Table 10 and Appendix B), and isdifficult to eliminate because of its popularitywith landscapers, ranchers, and landowners. Theproblem with eucalyptus is its allelopathic effect:as eucalyptus leaves drop and accumulate theychange the soil chemistry and prevent other plantspecies from growing. The chemicals in eucalyptusleaves sterilize the surrounding soil, an effectthat persists for years.Several willow species, Fremont cottonwoods,and valley oaks deserve further discussionbecause of their habitat value, dominance, orrarity. Willows along the Tuolumne River occur ineither shrub form (e.g., narrow leaf willow), ortree form (e.g., Goodding's black willow). Sincethe NDPP was completed, the reduced high flowregime has favored narrow-leaf willow becausethey have the longest seed dispersal period whichoverlaps with stable summer base flows, and theyare well adapted to survive infrequent high energyconditions. Narrow-leaf willow is a shrub type,grows in dense monotypic stands, and was themost abundant of all willow species mapped.Narrow-leaf willow is problematic in manyreaches due to its ability to easily colonizeriverbanks, create riparian berms, and reducefloodwater access to floodplains. The only othershrub willow common throughout the entire lowerriver was arroyo willow. It was often the dominantor co-dominant plant species within a series.Arroyo willow is far more common in the gravelbeddedzone than the sand-bedded zone.Tree willow species are dominated by Gooding'sblack willow because it is best adapted to theartificially dryer microclimatic conditions causedby riparian vegetation clearing. It is the mostabundant tree willow and is the dominant speciesin many stands. Pacific willow and red willow arefar less abundant, and were documented only assub-dominant plants in other vegetation series.Fremont cottonwood is commonly observedwithin the lower Tuolumne River corridor, butnearly all stands and individuals are old andsenescent. The only exception was in the DredgerTailing Reach (Reach 6), where remnant dredgerponds have allowed cottonwoods to regenerate.The general absence of young cottonwood cohortis troublesome because senescent cottonwoodshave already made most of their ecologicalcontribution (detritus and seed production), andare no longer growing and producing large seedquantities. Without younger age classes, dyingtrees cannot be replaced, and additional significantlosses to mature cottonwood stands areimminent. This attrition process has beenobserved on other regulated alluvial rivers,potentially leading to the collapse of a river'scottonwood stands (Merigliano, 1996). The bestCHAPTER 3123

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORTable 3-10. Total surface area of riparian vegetation series within the lower Tuolumne River corridor.CHAPTER 3Total Area(acres)MaximumPatch Size(acres)MinimumPatch Size(acres)Number ofpatchesNative Riparian Arroyo willow 4.1 1.02 0.11 9Black willow 230.6 15.67 0.01 210Blue elderberry 1.4 0.24 0.02 16Box elder 112.8 5.76 0.03 148Button bush 3.0 0.46 0.01 18California buckeye 10.1 6.47 0.05 6California grape (Vitis californica )* 0.7 0.33 0.14 3California walnut (Juglans nigra )* 13.8 12.02 0.03 8Dusky willow 4.2 1.22 0.02 17Fremont cottonwood 456.6 21.58 0.00 449Mixed willow 148.5 6.64 0.06 142Narrow-leaf willow 514.7 10.71 0.02 617Oregon ash 7.0 1.39 0.01 24Pacific willow 4.8 1.65 0.02 9Valley oak 620.5 44.53 0.02 439Western sycamore (Platanus racemosa )* 0.1 0.05 0.01 2White alder 30.6 3.12 0.01 88TOTAL 2163.4 44.53 0.00 2205Native upland Blue oak 33.9 12.90 0.03 21Bush lupine (Lupinus sp. )* 2.3 1.87 0.43 2Interior live oak 101.2 92.48 0.07 11TOTAL 137.4 92.48 0.03 34Emergent TOTAL 40.9 6.27 0.02 72Exotic Black locust (Robinia psuedoacacia )* 0.1 0.13 0.13 1Disturbed/miscellaneous exotics 6.3 3.72 0.28 5Edible fig 1.5 0.73 0.06 3English walnut (Juglans regia )* 1.9 1.46 0.08 5Eucalyptus 11.7 5.05 0.03 13Giant reed 5.2 0.65 0.01 47Himalayan berry (Rubus discolor )* 3.6 0.79 0.07 15Lamb’s quarters 1.0 0.96 0.96 1Tamarisk (Tamarix sp.)* 0.2 0.14 0.02 2Tree of heaven 8.4 2.23 0.03 18Tree tobacco (Nicotiana glauca )* 2.7 0.66 0.15 8Weeping willow (Salix babylonica )* 0.7 0.25 0.22 3TOTAL 43.1 5.05 0.01 121TOTAL 2384.9 92.48 0.00 2432* Not defined as a vegetation series because they are individual plants, groups of individuals,or has no overstory.124

GEOMORPHIC AND RIPARIAN INVESTIGATIONSexample is the Deardorff reach from RM 35.2 to35.6, which is virtually the only reach along theentire river that has not been significantly alteredby land conversion. The pre-dam floodplain andriparian forests were still intact in the early 1990'sand extensively used by herons and egrets as arookery (Trinity Restoration Associates 1991).Since then, attrition from old-age and fire haveeliminated most of the mature cottonwoods, andthe floodplain is slowly converting to tree ofheaven and grassland. Additionally, as thesemature cottonwoods die, a primary seed sourcedies with them. Restoring cottonwood standsshould therefore be an integral component of allchannel and floodplain restoration projects.Valley oaks are also found throughout theTuolumne River corridor, and are usually thedominant plant in a series. Because of their slowgrowth, valley oaks are one of the most threatenednative riparian species in the corridor and CentralValley. Valley oak regeneration on the TuolumneRiver is more successful than the Fremontcottonwoods, partly because valley oaks are not asdependent on fluvial processes for regeneration.Additionally, valley oaks regenerate better onheavier soils with a high silt and clay content.Animals stashing acorns (jays, squirrels) assistvalley oak regeneration.Urban, agricultural, and aggregate extraction landconversion adjacent to valley oak stands havereduced populations of those animals that stashacorns where they could germinate if forgotten,and continual disturbance prevents those acornsthat do sprout from maturing. Additionally, theregulated flood flow regime has reduced, if noteliminated floodplain formation processes and thesilt and clay deposition floodplains and terraces.There are several pockets of naturally reproducingvalley oak stands, but many stands are senescent.Valley oaks appear to be regenerating in the fewplaces within the corridor where acorns arefluvially deposited and in partially shaded standswith fluvial silts and clays intact. Riparian series mapping and riparianinventoryDuring September and October of 1996 weconducted a field-based inventory of riparianvegetation series within the Tuolumne Rivercorridor from La Grange Dam (RM 52.2) to theSan Joaquin River (RM 0.0). Riparian vegetationwas mapped by series on low altitude aerialphotographs during several weeks of fieldreconnaissance. This method provided accuratespatial boundaries of vegetation, as well asverified species/series identification. We mappedvegetation on three air photo sequences: 1986(1:2,400) from La Grange Dam (RM 52.0) toGeer Road Bridge (RM 26.0) enlarged 1993(1:4,000) from Geer Road Bridge (RM 26.0) tothe San Joaquin River confluence (RM 0.0), and1997 (1:2,000) for off channel riparian areas.Vegetation was mapped by tracing boundariesaround distinct sub-units on the photographs. Wealso noted the disturbance level of parcels, thetype of disturbance (e.g., grazing, urban encroachment,etc), and identified potential riparianrestoration and preservation sites. However, wedid not differentiate quality of individual stands;degradation was related more to land parcels andland use rather than stand types. We then calibratedaerial photographs to control pointscommon to the existing GIS maintained by theDistricts, digitized the riparian series boundaries,and riparian restoration and preservation sites asunique GIS layers.Not surprisingly, our primary finding was that thetotal acreage of riparian vegetation in theTuolumne River corridor has been vastly reduced.Prior to extensive land development there were anestimated 13,000 or more acres of riparianvegetation between La Grange and Modesto.Today less than 2,200 acres remain between LaGrange and the San Joaquin River (Table 3-10).A second finding was a transition between whitealder and box elder near Geer Road Bridge (RM25). White alder is common along the low flowchannel in the gravel-bedded zone, but theirdistribution ends near Geer Road Bridge, and theyare replaced by box elder, which continuedownstream to the San Joaquin River. Thistransition is largely due to the decrease in channelslope and transition from gravel bedded to sandbedded substrate. Apparently, alders prefer graveldominated substrate, while box elders prefer sanddominated substrate. Both tend to occupy asimilar hydrologic niche along the low flowchannel margins.We also found that most relic riparian vegetationstands greater than 10 acres were typically withinState Park boundaries, the City of Modesto, orStanislaus County parks. However, these relicstands have not been immune to human distur-CHAPTER 3125

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 3bance. Roads and campgrounds create openings inan otherwise dense understory, and frequentground disturbance (vehicular and foot traffic,lawn maintenance) discourages natural regenerationprocesses. High intensity human activity alsodiscourages wildlife use. Park management oftentends to prevent a relic stand from changing,resulting in no new riparian recruitment andcontinued aging and dying-off of senescentriparian stands. The few remaining relic standson private property (e.g., Deardorff's at RM 35.2)have considerably more wildlife use, which maybe related to less intensive management ordisturbance.Riparian mapping also distinguished vegetationin different geomorphic sub-units. The followingdescriptions of riparian stands in each sub-reachillustrate these unique characteristics.3.4.2. Description of riparian vegetationin Sand-bedded ZoneVegetation in the sand-bedded zone was historicallysubjected to somewhat different processesthan the gravel-bedded zone. Rather than thechannel migrating and/or avulsing back and forthbetween two valley walls, the channel in the sandbeddedzone tended to migrate slowly, increasingthe meander amplitude to a pivotal point at whichthe meander would cut off. This migrationalprocess eroded mature riparian vegetation on theoutsides of bends, and built new floodplains onthe insides of the bends. As meander bends werepinched off, they created oxbows that wereseasonally hydrated by the groundwater table.Oxbows and developing floodplains providedideal conditions for riparian initiation andgrowth. The availability of silts and clays on thefloodplain created fine-textured soils that couldsupport large stands of valley oaks. These sitesmight not be disturbed by floods or channelmigration for many decades, allowing them tomature into large gallery forests (hundreds ofacres) (Figure 2-17 and 2-27). Gallery forestsappear to have had almost total canopy closure,creating unique and diverse microclimates in theTuolumne River bottomlands. Young islandsmight have cottonwood and valley oak providingthe stand structure, and become surrounded bywillow thickets. Over time, vines would grow onthe maturing overstory trees, and by the time theoverstory became senescent or vines had begun toshade out the canopy trees, the river presumablywould again erode into the gallery forest andcontinue the process elsewhere.Conditions necessary for maintaining theseprocesses, and the riparian vegetation dependentupon these processes, have largely been eliminated.Rip-raping and reduced high flow regimeprevent the channel from migrating, such thatoxbows and floodplains are no longer created.Several relic oxbow lakes remain as testament toa greater forest that was once present (Figure 2-27), but they are now canal drains and irrigationponds. Black willow, narrow-leaf willow, and boxelder are the only tree species successfullyregenerating under contemporary conditions.Restoration designs should attempt to recreate thedense vegetation that was historically found in thesand-bedded zone; vegetative cover appeared tobe complete over most of the zone. Revegetationefforts should attempt to establish completevegetative cover as soon as possible followingplanting (within ten years). The Nature Conservancyeffectively employs conventional farmingtechniques on the Cosumnes and SacramentoRivers, using either variably spaced rows orpseudo sine waves. Cottonwoods should beprioritized because of their fast growth, whilevalley oaks could be planted between cottonwoods,to eventually grow over the cottonwoodcanopy. Reach 1: Lower Sand-bedded Reach(RM 0.0 to 10.4)Most riparian vegetation in the lower sandbeddedreach has been cleared (Figure 2-23 and2-24), leaving a narrow band one tree-width widebetween agricultural lands and the river. Thesestrips of one tree width sometimes link largerrelic valley oak and cottonwood stands. From theconfluence with the San Joaquin River to RM10.4 there are few large (>5 acres) stands ofriparian vegetation, with only a small percentageof valley oak (Appendix B, Maps 16-19). Thenewly acquired San Joaquin Wildlife Refuge atthe downstream end of the reach contains some ofthe best remaining riparian forests in the SanJoaquin basin.Over the past few decades, bank rip-rap andincreasingly regulated flow regimes have stabilizedthe banks in what was once a frequentlymigrating channel. Stabilization encouraged atrapezoidal channel geometry, prevented channel126

GEOMORPHIC AND RIPARIAN INVESTIGATIONSmigration in most reaches, reduced naturalriparian regeneration, and eliminated meandercutoffs (and associated oxbows). Riparianregeneration in this area is limited to localpockets in the rip-rap, or on the upper edge oflevees. Relic valley oak and cottonwood standsremain around old oxbow channels, and representthe greatest cover and structural diversity betweenthe City of Modesto and the river's confluencewith the San Joaquin. On the Mapes Ranch at RM0.5, where the channel is still migrating and highspring flows can access a floodplain, cottonwoodsare regenerating. This site is discussed inmore detail in Section Remnant standsshould be longitudinally and laterally enlarged,and eventually connected with the Tuolumne RiverRegional Park (upstream) and the San JoaquinWildlife Refuge downstream. Reach 2: Urban Sand-bedded Reach(RM 10.5 to RM 19.3)This reach is dominated by the Tuolumne RiverRegional Park, and urban expansion into theTuolumne River corridor in areas surrounding thePark. Because of continued urban expansion,riparian vegetation outside the Tuolumne RiverRegional Park is dwindling. Outside of the park,riparian vegetation consists of small (5 acres) ofvalley oaks and cottonwoods. Narrow-leaf willowseries dominates riparian vegetation (Appendix Bmaps 11-13). River confinement between thebluffs is more pronounced in this reach, as isnarrow-leaf willow encroachment into the activechannel. Along the base of the bluffs, stands ofvalley oak and mixed willow series thrive,presumably sustained by seeps along the base ofthe bluffs. Continued agricultural encroachment,urban development, and the reduced high flowregime discourage riparian vegetation fromregenerating.3.4.3. Description of riparian vegetationin Gravel-bedded ZoneAs discussed in Chapter 2, the historical highflow regime, low flow regime, adequate sedimentsupply, and bankfull/floodway confinementprovided the "checks and balances" to preventriparian vegetation from establishing a densejungle between valley wall margins. Riparianvegetation tended to establish on areas with heavysoils (silts) and shallow water tables. In thegravel-bedded zone, these areas were at the baseof bluffs and terraces where groundwater moistenedsilty soils, or in remnant channels, sidechannels, or floodplain surfaces where topographicaldepressions created zones close to thegroundwater table. Riparian vegetation tended tokey into these two microclimates, resulting inpatchy distributions and abundances (Figures2-19). These patches were true riparian forest.Between patches, floodplains were primarilygrasslands, with occasional valley oaks.Today, little of the original vegetation remains inthe gravel bedded reach due to agriculturalencroachment and aggregate extraction; allregenerating hardwoods are contained within thenarrow 9,000 cfs floodway. Nearly all areas thatCHAPTER 3127

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 3naturally supported riparian forests have beenmined, grazed, and/or farmed. The only nativeriparian species that has benefited from land useactivities and flow/sediment regulation is narrowleafwillow. Reproductively they are very aggressive:underground runners and plant fragmentsgive narrow-leaf willows an incomparable abilityto reproduce independent of fluvial processes. Asa result, much of the gravel-bedded reach notsubject to continual human disturbance hasnarrow-leaf willow encroachment. Encroachment isso extensive in some areas that the channel cannotmigrate. Riparian regeneration also is prevented inmany areas by extensive cattle grazing.Restoration designs within the gravel-bedded zoneshould reflect riparian vegetation's patchiness;complete vegetative cover did not naturally occurdue to soil texture and moisture variations.Because of the natural spatial variation invegetation, plant series should be planted inpatches, leaving open space in between thepatches. Special attention should be given tosprings, seeps, and the summer ground waterelevation, because we can target revegetation inthese areas that will improve the long termsuccess of riparian revegetation efforts. Reach 4: In-channel Gravel MiningReach (RM 24.0 to 34.2)Primary impacts to riparian vegetation is from inchannelgravel mining and cattle grazing, whichhave reduced the riparian corridor width andspecies diversity from historic conditions.Consequently, riparian vegetation regenerationhas been eliminated, other than asexual reproductionby narrow-leaf willow. The diversity inriparian series types has also decreased (AppendixB Maps 7-11). For example, between RM 29.0and 34.2, over 90% of mapped vegetation belongsto mixed willow or narrow-leaf willow series.Valley oaks and cottonwoods are isolated individuals,or stands with no connection to otherriparian stands. Exotic species cover is extensive,and in some locations (RM 25.0) cover the entireright bank for over 1,500 ft.The downstream end of this reach marks thetransition from gravel-bedded river to a sandbeddedriver. A corresponding plant seriestransition correlates with this change in substrateand channel slope. White alder series, common ingravel-bedded reaches upstream, becomesincreasingly less common in the gravel-bed/sandbedtransition, and is eventually replaced by boxelder downstream. White alder and box elderoccupy channel margins in riffles and the outsidesof meander bends.At the upstream extent of this reach (RM 31.8 to34.2) where the channel is confined againstbluffs, land use in the corridor has been minimalbecause of the narrow corridor width. This hasresulted in the largest contiguous stand of valleyoaks on the Tuolumne River. Reach 5: Gravel Mining Reach (RM34.2 to 40.3)Off-channel aggregate extraction and some inchannelaggregate extraction have dictated whereriparian vegetation can grow in this reach,creating a unique spatial pattern (Appendix B,maps 5-7). Pre-NDPP floodplains were mined,removing all riparian vegetation and leaving offchannelpits isolated from the Tuolumne River bydikes. Riparian regeneration is almost exclusivelynarrow-leaf willow and white alder, inhabitinglow-water margins of the dikes along both banks.Aggregate extraction has left solitary valley oaksor cottonwoods often surrounded by exotic plants.The south bank has been severely disturbed, withlengths of unvegetated channel commonlyexceeding 1,000 ft. The primary limiting factor inthis reach is floodway space; dike setbacks andfloodplain restoration are essential to increasingriparian vegetation in this reach. Reach 6: Dredger Tailing Reach (RM40.3-45.5)This reach is the widest among the gravel-beddedreaches. Vegetation flourishes along the channeland in hollows created by dredger tailings(Appendix B Maps 4-5). Turlock Reservoir StatePark (RM 41.0) contains a large relic valley oak/cottonwood stand (> 5 acres), perhaps the bestexample of mature riparian vegetation structureand species composition in the gravel-beddedzone. These cottonwood and valley oak stands arehighly productive and could be a seed source forfuture restoration. This is the only reach wheremultiple age classes of cottonwoods weredocumented, suggesting that little regeneration isoccurring. Younger age classes are establishingprimarily between rows of dredger tailing moundswhere groundwater is near the surface. However,128

GEOMORPHIC AND RIPARIAN INVESTIGATIONSthere is little continuity between stands becausethese mounds tend to separate the patches ofriparian vegetation.A dense thicket of arroyo willow and/or narrowleafwillow within the historic bankfull channel isthe only other regenerating riparian vegetation. Ina few areas along this reach, cattle grazing hasprevented riparian regeneration and denuded thebanks. The understory and gaps within relicFremont cottonwood and valley oak stands arebeing invaded by tree of heaven and giant reed.When the NDPP was constructed, much of theconstruction aggregate was removed fromReaches 6 and 7. Removing the dredger tailingslowered surfaces adjacent to the river to nearcontemporary floodplain elevations. There istremendous opportunity for both artificial andnatural riparian regeneration in this reach. Reach 7: Dominant Spawning Reach(45.5-52.1)The downstream section of this reach is confinedby valley walls and terraces (RM 45.5 to RM47.5), that supports a relatively narrow band ofriparian. The section upstream of Dominici Creekwidens into a 1,000 ft or wider corridor, andagain narrows at RM 50.5 at the "official"beginning of the Sierra Nevada foothills. Theriparian corridor width varies with valley width(Appendix B, Maps 1-3). Dredger tailings werealso removed for the NDPP, and subsequentchannel reconstruction in 1971 created a widespawning channel with low confinement andfrequently inundated floodplain. The channelmorphology has not changed significantly since1971, and riparian vegetation is typified by stripsof alder and narrow-leaf willow along the channelmargins, with scattered patches of narrow-leafwillow in remnant dredger tailing pits. SenescentFremont cottonwoods are also present, butyounger age classes of cottonwoods and valleyoaks are not. The middle section of the reach hasconsiderable potential for riparian restoration dueto low, frequently inundated floodplain surfaces,and potential elimination of cattle grazing.Upstream of Old La Grange Bridge (RM 50.5),the Tuolumne River is confined to a bedrockvalley. Riparian vegetation persists in hollows andcracks along the valley walls, and does not havethe wide areal extent observed downstream.Upland plant series including interior live oak,California buckeye, and blue oak stands dominatethe narrow riparian corridor within the bedrockvalley.3.4.4. Riparian vegetation relationshipsto contemporary and historic fluvialgeomorphologyAs discussed in Chapter 2, there are strongspecies-specific relationships between riparianvegetation, hydrology, soils, and geomorphicsurfaces. Flow and sediment regulation, combinedwith extensive land use, often obscures ordestroys these natural relationships. If flow andsediment regulation is so severe that the channelcannot adjust its dimensions, geomorphicsurfaces (bars, floodplains, and terraces) arefossilized by riparian plant encroachment. In mostalluvial rivers with unimpaired flow regimes,floods with recurrence intervals of 1.5 to 2.5years typically inundate floodplains. Floods ofthis recurrence interval approximate bankfulldischarge. We used this relationship in Chapter 2to illustrate how the reduced flood regime hasaffected riparian plant series initiation andestablishment. Pre-NDPP floodplain surfaces thatare no longer inundated cannot support floodplainvegetation regeneration.We compared relic and contemporary stands withpast and present fluvial geomorphic conditions inwhich they live. These relationships are useful infuture channel and riparian restoration projectsbecause the revegetation can be scaled accordingto the design discharges and planformmorphology; similar to scaling down channelmorphology to match a reduced flow regime.Vegetation transects were used to illustratethese relationships. Vegetation transectsWe surveyed a transect in the upper gravel-beddedreach, the upper sand-bedded reach, and lowersand-bedded reach. Each cross section hadriparian regeneration and represented differentchannel morphologies. Our objectives were to: (1)observe riparian and fluvial geomorphic relationshipsthat could be used for future restorationdesigns and (2) determine if the channel morphologyand riparian initiation patterns haveadjusted to the post-NDPP regulated flow regime.CHAPTER 3129

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 3The transect sampling sites were located at:• Basso Bridge transect (RM 47.0 in Reach 7),0.5 miles downstream of Basso Bridge, (Figure3-33).• Santa Fe transect (RM 22.5 in Reach 3), 0.3mile upstream of Santa Fe Bridge at LakewoodMemorial Park (Figure 3-34).• Confluence transect (RM 0.5 in Reach 1), 0.5miles upstream of the confluence with the SanJoaquin River on the USFWS National WildlifeRefuge (Figure 3-35).Each transect was established perpendicular tohigh flow direction. Vegetation was sampledwithin a 10 ft band upstream and downstream ofthe transect. Transect sampling included measurementsof stand age, diameter and tree heightsgreater than 6 inches breast height diameter(DBH), and species. Voucher specimens ofcommon native riparian and exotic hardwoodswere collected and have been archived by TIDand Fresno State University. The Confluencetransect was surveyed to 1929 NGVD as establishedby the Department of Water Resourcesduring their 1997 flood elevation surveys. Theother two transects used a relative datum of100.00' on the upper left bank transect headpin.Water surface elevation, flood debris elevation,and certain individuals trees and plants weresurveyed.One task was to associate riparian stand characteristicswith discharges that inundated distinctgeomorphic surfaces. We used flood debris, highflow water surface profiles, and U.S. GeologicalService discharge rating tables from the closestgage to quantify the stage and discharge forinundation. For the Basso Bridge transect, weused the La Grange gage (USGS Station # 11-289650) and our Basso Bridge water surfaceprofile survey (5,400 cfs); for the Santa Fetransect and the Confluence transect, we used theModesto gage (USGS Station # 11-290000),although water surface at the confluence transectis often governed by flows in the San JoaquinRiver.Basso Bridge Transect (RM 46.0)We chose the Basso Bridge transect because ofrelic pre-NDPP, valley oak, and Fremont cottonwoodstands on both banks and because weobserved some post-NDPP cottonwood and valleyoak regeneration (Figure 3-36 and 3-37). Miningactivities prior to the 1937 aerial photo seriesremoved all riparian vegetation on the left bank butavoided a few valley oaks on the right bank. By the1950 photo series, riparian vegetation was recoveringfrom mining. Cottonwood and valley oakstands were evident on aerial photographs. In thelate 1960's the left bank was excavated to near apost-NDPP floodplain elevation (a 5,400 cfswater surface and 2.5 year flood) for NDPPconstruction, and removal of left bank dredgertailings avoided most mature riparian vegetation.Riparian vegetation along this transect consists ofFremont cottonwoods, valley oak, and narrow-leafwillow series. Mature Fremont cottonwoods sitatop "islands" left when the dredger tailings wereremoved around the cottonwoods on the left bank(Figure 3-36). Valley oaks and cottonwoods areregenerating on the new "floodplain" surface onthe left bank; however, the right bank is heavilygrazed, preventing riparian hardwood regenerationeven though it is at an elevation approximating apost-NDPP floodplain. The mature valley oak andcottonwood stands on this transect are veryhealthy. The valley oak canopy is contiguous andhas approximately 60% canopy closure (Figure 3-37), but mature cottonwoods are not closeenough to each other to form a contiguous andclosed canopy.The rooting elevations for valley oak and cottonwoodsof different cohorts (pre- versus post-NDPPestablishment) shows that pre-NDPP cottonwoodsinitiated on pre-NDPP floodplain surfaces(inundated by 8,400 cfs, a 1.5 year recurrencepost-NDPP flood) (Figure 3-36). Post-NDPPcottonwoods initiated between the 5,600 cfs watersurface elevation and the 8,000 cfs water surface,which are 2.7 year and 5.6 year post-NDPP floodsrespectively. Channel migration does not occur inthis reach due to riparian encroachment andreduced high flow regime, and post-NDPP"floodplain" surfaces are not fluvially formed (butare excavated surfaces). Therefore, post-NDPPriparian regeneration is occurring on a artificiallyconstructed surface, which happens to inundateduring floods slightly larger than the 1.5 yearflood. Valley oaks, regardless of cohort, appear toregenerate at a variety of elevations above the5,600 cfs water surface elevation.Santa Fe Transect (RM 22.5)We chose the Santa Fe transect because of a largestand (4.25 acres) of mature Fremont cottonwoodson a pre-NDPP floodplain on the south130

GEOMORPHIC AND RIPARIAN INVESTIGATIONSTuolumne RiverFlowHWY132LAKEROADBASSO BRTRANSECTCHAPTER 3NFigure 3-33. Basso Bridge vegetation transect location (RM 47.0), shownon 1993 aerial photograph (approximate scale: 1” = 350’).bank, and because valley oaks and cottonwoodsare regenerating on a newly forming floodplain(Figures 3-34, 3-38, 3-39, and 3-40). The 1937and 1950 air photos show an orchard on the southbank floodplain; 1963 and 1974 photos show theorchard had been removed. At some pointbetween 1963 and 1974, a series of events(predicated on the fallowing old orchard)produced a successful cohort of cottonwoodsto establish. The transect shows the pattern ofpre- and post-NDPP riparian regeneration,species composition, stand structure, andcanopy architecture because it is one of the fewsites where the reduced hydrologic regime hasformed post-NDPP floodplains and the riparian131

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORSANTA FETRANSECTSANTA FE BRIDGECHAPTER 3NTuolumne RiverFlowFigure 3-34. Santa Fe vegetation transect location (RM 22.5), shown on 1993 aerial photograph (approximatescale: 1” = 350’).vegetation has partially regenerated. Riparianvegetation along the transect is diverse, consistingof four series: narrow-leaf willow, box elder,Fremont cottonwood, and valley oak.Currently, riparian regeneration is restricted tothe left bank between the low water edge and themature box elder stand (Figure 3-38); an area 250ft wide representing the zone of developing post-NDPP floodplain. This observation suggests thatriparian hardwood regeneration can occur ondeveloping floodplains that are inundated byfloods of 1.5 to 5 year recurrence intervals underthe post-NDPP high flow regime. In other words,the channel and riparian vegetation appears to bescaling down to the post-NDPP flow regime atthis location. When the transect was originallysurveyed in 1996, cottonwood seedlings initiatedclose to the summer water surface and valley oakswere establishing further up the bank, but stillwell within the post-dam bankfull channel. Whenwe resurveyed the transect after the January 1997flood, the cottonwood seedlings had been killedby the flood, but the establishing valley oaks werestill present.Canopy closure within the mature Fremontcottonwood stand is almost 100% and is contiguous.There is no liana (vines) development withinthe stand, and valley oaks in the area have notreached a "weeping" habit indicative of olderundisturbed stands. The Fremont cottonwoodunderstory (i.e., shrub and ground vegetationlayer under the cottonwoods) is open with onlygrasses in the ground layer. Along the bluffwalls, superimposed over the cottonwood's132

GEOMORPHIC AND RIPARIAN INVESTIGATIONSSan JoaquinRiver FlowTuolumneRiver FlowCONFLUENCETRANSECTSan JoaquinRiver FlowCHAPTER 3NFigure 3-35. Confluence vegetation transect location (RM 0.5), shownon 1993 aerial photograph (approximate scale: 1” = 700’).canopy, are mature valley oaks. On the historicfloodplain margin towards the bankfull channel, a20 ft tall, dense narrow-leaf willow thickettransitions into a mature box elder stand (Figure3-39). The narrow-leaf willow canopy is dense,with a short break before the open box eldercanopy. Another stand of narrow-leaf willow isgrowing on the evolving point bar near the lowflow water surface.This transect shows that pre-NDPP riparianvegetation established and matured on the historicfloodplains, while younger post-NDPP riparianvegetation is regenerating on post-NDPP floodplains,which are within the pre-NDPP bankfullchannel. These data suggest that regenerationcan occur at other reaches, but on a smaller scalewithin the historic bankfull channel, and perhapsonly at sites where channel migration allows thechannel to re-form a post-NDPP bankfull channel133

134Relative elevation (ft)140130120110100908070Left bank looking downstreamFloodplain and area ofriparian regenerationCHAPTER 34/7/97 Ground Surface4/7/97 Ground Surface 50 feet Upstream4/7/97 Water Surface (Q= 330 cfs)1/4/97 Water Surface (Q= 52,000 cfs)Estimated 5,600 cfs water surface elevationPre-NDPP valley oakPost-NDPP valley oak saplingsPre-NDPP cottonwoodPost-NDPP cottonwood600 75 150 225 300 375 450 525 600 675 750 825 900 975 1050 1125Distance from left bank headpin (ft)FloodplainRight bankTerrace/PastureTUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORFigure 3-36. Cross section servey and location of riparian vegetation at Basso Bridge vegetation transect (RM47.0)

GEOMORPHIC AND RIPARIAN INVESTIGATIONSFigure 3-37. Basso Bridge vegetation transect looking from left bank toward right bank.and floodplain. We do not expect cottonwoods toregenerate on pre-NDPP floodplains (which arenow terraces) because contemporary flows areinadequate to create gaps in the existing vegetation(to establish seed beds) and maintain soilmoisture during the seeding initiation period.There are few reaches that are migrating andforming a smaller two-stage channel under thecontemporary flow regime.Confluence Transect (RM 0.5)The Confluence transect exemplifies the lowersand-bedded reach riparian corridor. We chosethis reach because the landowner had ceasedcultivating the north bank floodplain, allowingriparian initiation to occur and the river tomigrate. A dike confines the river on the leftbank, with a tomato field behind it and a densethicket of willows growing between the dike andthe river (Figure 3-41 and 3-42). This site was anactively building point bar surrounded by denseriparian forest before agriculture cleared the area(Figure 2-27). Floodplain surfaces in this reachcontinued to regularly flood after NDPP wascompleted, but agricultural cultivation continued,preventing riparian regeneration from occurring.After cultivation and bank protection ceased, thechannel resumed migrating towards the right bank,creating a new point bar and incipient floodplainsurface on the left bank.Relating vegetation establishment elevations andgeomorphic surfaces with high flows is difficultin the lower sand-bedded reach because watersurface elevations depend on both TuolumneRiver flows and San Joaquin River flows. Whenthe San Joaquin River floods, the Tuolumne Riverbecomes a sluggish backwater. When TuolumneRiver flows exceed 8,500 cfs, all surfaces begin tobecome inundated. For Tuolumne River flows lessthan 7,000 cfs, the floodway in this reach is 600ft; when flows exceed 8,500 cfs, the floodwayexceeds 3,000 ft.There are no canopy forming trees along theConfluence transect. The dominant vegetationalong the transect consisted of Goodding's blackwillow and narrow-leaf willow. These specieswere concentrated within the bankfull channel(Stations 0 to 350 on Figure 3-41). Box elderand cottonwoods were present on the transect, butbox elder was only associated with the matureCHAPTER 3135

CHAPTER 3136Relative elevation (ft)140130120110100908070Left bank looking downstreamValley WallTerrace- Pre-NDPP & 4.25 acre Fremont cottonwood standPre-NDPP a flood with a 3 year recurrence interval inundated this surface,post- NDPP, the same maginitude flood has a 7.5 year recurrence interval.4/7/97 Ground Surface4/7/97 Water Surface Q= 330 cfs)1/4/97 Water Surface (Q= 52,000 cfs)Estimated 5,500 cfsAssumed pre-NDPP cottonwoodPost NDPP cottonwood seedlingsAssumed pre-NDPP Box elderPre-NDPP valley oakPost-NDPP valley oak saplingDevelopingFloodplainArea of post-NDPPriparian regenerationFloodplainRight banTerraTUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR60-775 -700 -625 -550 -475 -400 -325 -250 -175 -100 -25 50 125 200 275 350 425 500Distance from left bank headpin (ft)Figure 3-38. Relationship of cottonwood and valley oak trunk diameters to rooting elevations at Zanker model transect.

GEOMORPHIC AND RIPARIAN INVESTIGATIONSRoot collar ground surface elevation (Relativeelevation, ft)9998979695949392919089Pre-NDPP cottonwoodPost-NDPP cottonwoodPre-NDPP valley oakPost-NDPP valley oak saplingsLow water surface elevation (330 cfs)Post-NDPP floodplain elevation (5,600 cfs)Post-NDPP terrace elevation (8,429 cfs)880 5 10 15 20 25 30 35 40black willow stands on the south bank. Narrowleafwillow creates a dense jungle along the southbank, firmly anchoring a developing point bardeposit. Behind the narrow-leaf willow junglethere are Goodding's black willow trees with a boxelder understory; no trees grow over 20 feet high.Cottonwoods were establishing on the north bankfallow field. This fallow field was recentlyacquired by USFWS as part of the San JoaquinRiver Nation Wildlife refuge (Figure 3-41).Exotic annual plants currently dominate thissurface, but young (

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 3Figure 3-40. Photographs of Santa Fe vegetation transect (RM 22.5), looking from right to left bank at newlyforming floodplain in foreground of bottom photograph, and at pre-NDPP floodplain with mature cottonwoods in topphotograph and background of bottom photograph.138

GEOMORPHIC AND RIPARIAN INVESTIGATIONS807060Left bank looking downstreamRight bank4/11/97 Ground Surface4/11/97 Water Surface (Q= 350 cfs)Estimated 7,700 cfs water surface elevationAssumed pre-NDPP black willowPost-NDPP cottonwood seedlingsElevation (ft, msl)504030TomatoFieldContemporary Channel MigrationUSFWS NationalWildlife Refuge2010FloodplainPoint bar with blackwillow and narrow-leaf willowstandExposedsand barFloodplain & area ofcottonwood regeneration0-100 -25 50 125 200 275 350 425 500 575 650 725 800 875 950 1025 1100 1175Figure 3-41. Cross section survey and location of riparian vegetation at Confluence vegetation transect (RM 0.5).the narrower channel. We hypothesized thatriparian regeneration (particularly Goodding'sblack willow and Fremont cottonwood) dependson three fundamental processes: a migratingchannel that creates floodplain surfaces, floodinundation occurring between 1.5 to 5 years, and agently receding snowmelt hydrograph limb.Elimination of floods exceeding 10,000 cfs afterthe NDPP allowed narrow-leaf willow, box elder,and white alder to encroach onto the low flowchannel, while removal of the snowmelt hydrographresulted in xeric conditions on pre-NDPP floodplains. As a result, the ripariancorridor width narrowed and pre-NDPP cohortsof Fremont cottonwood and valley oak still aliveare beginning to die of old age. Riparian regenerationoccurs only where soil and microclimaticenvironments meet each hardwood species'physiologic requirements3.4.4.2. Planform vegetation patternsExamining pre-NDPP vegetation patterns andselected post-NDPP patterns from our transectsDistance from left bank headpin (ft)and riparian inventory maps allows us to hypothesizeplanform riparian vegetation patterns thatcan be used in future riparian revegetationdesigns. Most relic valley oak stands appear togrow above the 60,000 cfs water surface elevation,although there was still considerableregeneration between the 5,600 cfs water surfaceelevation and the 60,000 cfs water surfaceelevation, particularly in the gravel-bedded zone.Valley oak stands historically preferred terracesand floodplains areas that had heavy silt/claysoils. Today, valley oaks are only capable ofregenerating on contemporary floodplain surfacesand pre-NDPP floodplains (now functionalterraces).Relic Fremont cottonwood stands grow above the8,000 cfs water surface elevation on pre-NDPPfloodplains, with most growing above the 14,000-16,000 cfs water surface elevation. Contemporarycottonwood regeneration is dysfunctional,restricted to isolated reaches where channelmigration occurs, surfaces that have been loweredwhen removing dredger tailings, and pond marginsamong dredger tailing piles. Under naturalCHAPTER 3139

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 3Figure 3-42. Photographs of Confluence vegetation transect (RM 0.5), looking from right to left bank at newlyforming floodplain on bottom photograph, and looking from left to right bank at eroding bank on outside of meanderbend, top photograph.140

GEOMORPHIC AND RIPARIAN INVESTIGATIONSconditions, cottonwoods establish on floodplainswhere soil moisture and texture are "adequate".Adequate conditions are created by: topographicdepressions on floodplain surfaces that are closeto groundwater tables, snowmelt hydrographs thatmoisten floodplain soils during seeding periods,and exposed silty soils that retain moisture. Highflow scour channels, oxbows, and side channelsare common planform features where cottonwoodforests historically occurred.Goodding's black willow is a tree willow tolerantof a drier environment. Goodding's black willowtends to survive where agricultural or aggregateextraction encroachment has reduced riparianvegetation to one tree width. Naturally, however,they tend to grow near the bankfull channelelevation (on upper bars and lower floodplains),and grow well in topographic depressions in thefloodplain. Black willow grows below the 8,500cfs water surface elevation upstream of DryCreek, and below the 12,000 cfs water surfaceelevation below Dry Creek.White alder, narrow-leaf willow, and box elderare the primary species that have flourished underregulated flow and sediment conditions. Thesespecies grow along the channel margins betweenthe 300 cfs and the 6,000 cfs water surfaceelevations. Most narrow-leaf willow establishesbelow the 6,000 cfs water surface elevation andgrows down to the summer low water surface(

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 33.4.7. RecommendationsSeries that should be prioritized in restorationdesign are ones in which the "Nature ConservancyHabitat Status Index" ranking ends with"0.1" (Appendix B), including Fremont cottonwood,valley oak, and buttonbush series. Cottonwoodand valley oak series are particularlyimportant because of dramatic losses to agriculture,urban encroachment, and aggregate extraction.Cottonwood and valley oak series onceprovided substantial overstory habitat for birds(egrets, herons, osprey, bald eagles, and others),while the dense understory provided habitat forrodents (in particular the endangered riparianbrush rabbit). These series, particularly thecottonwoods, are not substantially reproducingnaturally due to land uses and lost fluvial processes.Additionally, blue elderberry series shouldbe prioritized for preservation and restorationbecause it provides critical habitat for the endangeredvalley elderberry longhorn beetle.Valley oak revegetation should be a strongcomponent of future channel and floodplainrestoration projects. The primary drawbacks tovalley oak revegetation are the high costs perplant, their slow growth rate, and high attritionrate (which is partly a result of their slowgrowth). Revegetation efforts should focus oncottonwood revegetation and native plant recruitmenton floodplain surfaces first, with valley oakrevegetation on the upper floodplain and terracesurfaces given second priority.The riparian corridor can be restored and maintained,but will require improved high flow eventsand will exist at a scale smaller than existedbefore the NDPP. We have established thatriparian vegetation requires sediment, floods, andspace to perpetuate its composition and structure.Fundamental Restoration Plan componentsrequired to restore the integrity of riparianvegetation will be:1. Develop a minimum 500 ft wide ripariancorridor and floodway along the entire riverthat is protected by conservation easements,private ownership, and/or public ownership.2. Preserve remaining valley oak and Fremontcottonwood stands to provide future seedsources (e.g., the valley oak stand at RM38.1-34.2, valley oak and cottonwoodstands at RM 47.3, the cottonwood stand atRM 6.8).3. Reconstruct floodplains and terraces at anelevation inundated by flows exceeding 4,000cfs to 6,000 cfs.4. Incorporate silt importation on floodplainrestoration projects wherever possible toimprove oil moisture retention and promotenatural regeneration.5. Reconstruct floodplains and terraces that aretopographically variable, to allow somedepressions a longer period of saturated soilconditions.6. Encourage channel migration at all siteswhere no human structures are at risk so thechannel can construct a contemporaryfloodplain.7. Target Fremont cottonwood and valley oak atriparian restoration projects to replace dyingpre-NDPP generations.8. Remove exotic plants wherever possible.9. Encourage floodplain inundation duringflood control releases to deposit fine sedimentand saturate floodplain soils.10. Increase flood flow magnitude and variabilityover different water years to create andmaintain topographic diversity on bars andfloodplains.11. During springtime flood control releases inwetter water years, maintain dam rampingrates less than 8 cm/day to facilitate cottonwoodseedling survival.12. Improve management of riparian zones thatwould encourage natural regeneration (e.g.,eliminate grazing, landscaping maintenancein parks, etc.).142

RESTORING THE TUOLUMNE RIVER CORRIDOR4. RESTORING THE TUOLUMNE RIVER CORRIDORDeveloping a restoration vision shared by allstakeholders is one of the primary functions ofthis report. In practice, however, rehabilitating orrestoring a river corridor has different meaningsfor different people, a situation that can lead toconsiderable dissention among stakeholders if nocommon vision is developed. A vision shared bystakeholders, on the other hand, reduces politicaldistractions, facilitates restoration and monitoringfunding decisions by identifying and prioritizingcommon goals.The Tuolumne River is a heavily managedsystem. A successfulrestoration strategy mustacknowledge that the riverwill never return tohistorical conditions in ourlifetimes. However,reversing more than acentury of environmentaldegradation and significantlyimproving thehealth of the river isessential. Developingspecific restoration goalsand a shared vision,appropriate strategies andapproaches, then identifyingpotential restorationsites and priority projects,are the first steps towardrestoring ecological healthand integrity to theTuolumne River. Implementationof the RestorationPlan and adaptivemanagement by theTRTAC will measurerestoration success.4.1. RESTORATION GOALS ANDOBJECTIVESAs discussed in Section 1.3.1, most past researchon the Tuolumne River focused on biologicalhabitat conditions, whereas fluvial and riparianprocesses are largely responsible for forming andmaintaining biological habitat, and thus must beincorporated into a comprehensive restorationapproach. In Chapter 2, we began our evaluationof fluvial and riparian processes by first developingthe Attributes of Alluvial River Integrity,which serve as quantitative and qualitativerestoration objectives. Then, in Chapter 3, webegan quantifying many of these attributes byevaluating the evolution and dynamics of the M.J.Ruddy Four Pumps Restoration Project (Attribute1), evaluating opportunities for improving floodpeak variability (Attribute 2), measuring andmodeling bed mobility (Attribute 3), measuringand modeling bedload transport rates (Attribute5), identifying bedload impedance reaches, andgravel introduction sites and sources (Attribute5), inventorying riparianvegetation from La GrangeDam to the San JoaquinRiver (Attribute 9), anddocumenting existing andremnant riparian standassociations with hydrologyand channel morphology(Attributes 2, 7, and9). These evaluationssupplemented the largebiological database thatexisted for the TuolumneRiver to strengthenrecommendations presentedin the RestorationPlan. Again, while theRestoration Plan targetschinook salmon as a keymanagement species, therestoration strategy isintended to improveconditions for a variety ofplant and animal populationswithin the TuolumneRiver corridor.4.1.1. Goals and objectives of existingrestoration programsSeveral restoration plans and programs have beendeveloped in the Central Valley, CA, over the lastseveral years. The various goals and objectives ofthese programs were considered during developmentof the Tuolumne River Restoration Plangoals and objectives.CHAPTER 4143

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER CDFG Restoring Central ValleyStreams: A Plan For ActionThe specific goals of the CDFG Plan, as presentedin Governor Pete Wilson’s April 1992 WaterPolicy Statement, are to restore and protectCalifornia’s aquatic ecosystems that support fishand wildlife, and to protect threatened andendangered species. The goals of this plan alsoincorporate the State-legislated mandate andpolicy to double 1988 population levels ofanadromous fish in California (Salmon, SteelheadTrout and Anadromous Fisheries Program Act,1988). This equates to an adult escapement targetof 12,600 chinook salmon on the Tuolumne River.The highest priority actions (A1) recommendedfor the Tuolumne River include: (1) restorespawning, rearing, and migration habitat, (2)require adequate streamflow releases for theprotection of salmon spawning, rearing, andoutmigration, (3) establish water quality objectivesfor the protection of spawning, rearing, andoutmigration, (4) evaluate effects of fluctuatingflows due to power peaking on salmon spawningand rearing, (5) evaluate fish screening needs,and (6) complete evaluation of spawning, rearing,and migration habitat restoration needs. USFWS Anadromous FishRestoration Program (AFRP)The AFRP was developed by the US Fish andWildlife Service in response to the 1992 CentralValley Project Improvement Act (CVPIA 1992),federal legislation that directed the Secretary ofthe Interior to develop and implement a programto restore anadromous fish populations to CentralValley streams. Specifically, the Secretary’smandate was:“develop within three years of enactment [of CVPIA]and implement a program which makes all reasonableefforts to ensure that, by the year 2002, naturalproduction of anadromous fish in the Central Valleyrivers and streams will be sustainable, on a long-termbasis, at levels not less than twice the average levelsattained during the period of 1967 to 1991…”The fall-run chinook salmon population target setby the AFRP for the Tuolumne River is 38,000returning adults. The program also establishedthat first priority be given to measures which“protect and restore natural channel and riparianhabitat values through habitat restoration actions”to ensure that both physical and biologicalecosystem components can resist declines andrecover from both natural and anthropogenicdisturbances. CALFED Ecosystem RestorationProgramThe CALFED Ecosystem Restoration ProgramPlan (ERPP) was developed to address theCALFED goal for ecosystem quality, which is “toimprove and increase aquatic and terrestrialhabitats and improve ecological functions in theBay-Delta to support sustainable populations ofdiverse and valuable plant and animal species.”The program is explicitly founded on rehabilitationof ecological processes associated withstreamflow, stream channels, floodplains andwatersheds throughout the Central Valley as anessential requirement for sustaining resilientpopulations of fish and wildlife, and thus representsa significant shift in strategy from singlespeciesmanagement.While one primary purpose of the CALFEDProgram is to ensure reliable water supplies forpresent and future consumptive uses, the FERCSettlement Agreement has precedence in determiningminimum streamflow requirements in theTuolumne River. Additionally, the FERC SettlementAgreement has provisions (Sec. 11 and 18)for supporting “Ancillary Programs” that includethe transfer of water for instream environmentaluses downstream of the dams.4.1.2. New Don Pedro Project FERCSettlement AgreementArticle 37 of the New Don Pedro Project License(No. 2299-024), issued by the Federal PowerCommission (later renamed the Federal EnergyRegulatory Commission, FERC) in 1964, requiredreevaluating the project’s minimum flowrequirements after the first 20 years of operation(the NDDP was completed in 1971). FERCinitiated this evaluation in 1994, and prepared aFinal Environmental Impact Statement (FERCFEIS 1996) in compliance with the NationalEnvironmental Policy Act (NEPA). The FEISevaluated a range of flow modifications and nonflowmitigation, which resulted in adoption of theFERC Settlement Agreement, entered into amongthe following Tuolumne River Stakeholdergroups:• California Department of Fish and Game(CDFG)144

RESTORING THE TUOLUMNE RIVER CORRIDOR• California Sports Fishing Protection Alliance(CSPA)• City and County of San Francisco (CCSF)• Federal Energy Regulatory Commission(FERC)• Friends of the Tuolumne (FOTT)• Modesto Irrigation District (MID)• San Francisco Bay Area Water Users Association(BAWUA)• Tuolumne River Expeditions (TRE)• Tuolumne River Preservation Trust (TRPT)• Turlock Irrigation District (TID)• U.S. Fish and Wildlife Service (USFWS)Participants agreed to support the SettlementAgreement, which provided a revised instreamflow schedule for NDPP operation (Table 2-5),and outlined a strategy for recovery of TuolumneRiver chinook salmon (Articles 8-13). Restorationobjectives listed in Sections 8-13 of the SettlementAgreement are:• Increase naturally occurring salmonpopulations.• Protect any remaining genetic distinction[among salmon populations].• Increase salmon habitat in the Tuolumne River.• Implement measures generally agreed upon asnecessary to improve chinook salmon habitatand increase salmon populations. Thesemeasures include increased flows (FSA FlowSchedule), habitat rehabilitation and improvement,and measures to improve smolt survival.• Implement additional measures of some riskthat the Technical Advisory Committee (TAC)agrees may help improve the population.• Use an adaptive management strategy thatwould initially employ measures consideredfeasible and have a high chance of success.• [Conduct a detailed annual review] to assessprogress toward meeting the goals described inthe Settlement Agreement.The Settlement Agreement stipulates that successof the flow modifications and non-flow mitigationmeasures will be re-evaluated again in 2005. ThisRestoration Plan represents the primary planningproduct of the Settlement Agreement, by cooperativelydeveloping a restoration vision (how do wewant the river corridor to function to best supportchinook salmon and other native species), as wellas identifying and prioritizing restorationprojects. The restoration vision, shared bystakeholders, is an essential component of anyrestoration effort because it provides focusedpolitical and technical committment towards acommon goal.4.1.3. River-wide restoration goalsAs illustrated in Chapter 2, salmonid life historystrategies have adapted to the natural hydrologicand fluvial processes on the Tuolumne River, andto the habitat conditions and biological communitiescreated and maintained by those processes.Accordingly, strategies for recovering andsustaining a robust chinook salmon populationmust be based on restoring fluvial processes toimprove ecological health and integrity to thefullest extent possible, given contemporarysediment and flow regimes. Restoring ecosystemprocesses provides for the life-history requirementsof salmon over the long term, as well as forother riverine species.The Tuolumne River has the greatest restorationpotential among the San Joaquin River tributariesfor several reasons. First, periodic high flowreleases for flood control operations can helprestore fluvial geomorphic functions to thechannel and alleviate riparian vegetation encroachment.A more variable streamflow schedulecan also improve chinook salmon habitat andhelp restore several life history phases. Additionally,management institutions and stakeholdergroups possess a broad ecological understandingof the Tuolumne River, and are committed to thegoal of ecosystem restoration and salmon recovery.Finally, with the infusion of restorationfunding for implementation, the Tuolumne Riverhas the tools necessary to improve the riverecosystem, and sustain a robust, naturallyproducing salmon population.The two biggest challenges facing restoration ofthe Tuolumne River are first, implementing acomprehensive Restoration Plan that includesshort-term and long-term strategies for restoringand managing the river, and second, minimizingimpacts of future development within the LowerTuolumne River corridor. Both challenges areinextricably linked. The restoration effort mustassess and work with future development withinthe river corridor, or restoration will continue toCHAPTER 4145

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 4follow in an attempt to mediate ongoing development,at considerable public expense. The 1997flood caused extensive damage to the river andsurrounding infrastructures, but it also increasedpublic awareness of the river, and illustrated thefundamental need for a wider floodway withlarger flood capacity. Public interest in promotingaesthetic and recreational values on the river hasalso increased. These factors have given us thetimely opportunity to implement a RestorationPlan that not only improves environmentalconditions along the river, but can also providebenefits to public and private infrastructure, andother public rsources, as well.Historical and contemporary impacts to theTuolumne River have far exceeded the river’scapacity for self-recovery in a timeframe acceptableto stakeholders. Therefore restoration willinitially require a large degree of active, mechanicalrestoration, such as filling in-channel pits,introducing spawning gravel by re-creating inchannelalluvial deposits, and revegetatingriparian zones. While acknowledging that theriver cannot be restored to its pristine condition,this Restoration Plan recommends this initial“jump-starting,” of active habitat restoration,followed by flow and sediment management thatre-establishes natural processes at a scale correspondingto contemporary sediment and hydrologicregimes. Inherent with any restorationprogram of this large scale is some degree ofuncertainty as to how effective, and within whattime-frame, restoration will be in contributingtoward chinook salmon recovery. Therefore,adaptive management must closely monitor andrefine restoration approaches to ensure successfulrecovery of natural chinook salmon production.The physical and biological attributes that definea healthy alluvial river change with longitudinaldistance as the Tuolumne River emerges from themountains and foothills of the Sierra NevadaRange and meanders through the Central Valley.For example, river behavior in a sand-beddedriver can be different than a gravel-bedded river.These attributes underpin the structure andfunction of the river ecosystem and determinelocal and reach-wide variation in river morphology.As described in Chapter 2, the lowerTuolumne River has two geomorphically distinctunits (Figure 4-1): a moderate gradient, gravelbeddedzone from La Grange Dam (RM 52.2)downstream to below Fox Grove County Park(RM 24), and a low gradient sand-bedded zoneextending to the confluence with the San JoaquinRiver (RM 0). These two zones are divided into 7reaches characterized by general restoration needsthat resulted from current and historic land usepractices.River-wide restoration goals for theTuolumne River include:• A continuous river floodway from La GrangeDam to the confluence with the San JoaquinRiver with capacity that safely conveys at least15,000 cfs above Dry Creek and 20,000 cfsbelow Dry Creek;• A continuous riparian corridor from La GrangeDam to the San Joaquin River confluence, witha width exceeding 500 ft minimum in thegravel-bedded zone to a width up to 2,000 ftnear the San Joaquin River;• A dynamic alluvial channel, maintained byflood hydrographs of variable magnitude andfrequency adequate to periodically initiatefluvial geomorphic processes (e.g., mobilizechannelbed surface, scour and replenish gravelbars, inundate floodplains, and promotechannel migration);• Variable streamflows, such as during chinookspawning, rearing and emigration, to benefitsalmon and other aquatic resources;• A secure gravel supply to replace graveltransported by the high flow regime, thusmaintaining the quantity and quality of alluvialdeposits that provide chinook salmon habitat;• Bedload transport continuity throughout allreaches;• Chinook salmon habitat created and maintainedby natural processes, sustaining a resilient,naturally reproducing chinook salmon population;• Self-sustaining, dynamic, native woody riparianvegetation;• Continual revision of the adaptive managementprogram, addressing areas of scientific uncertaintythat will improve our understanding ofriver ecosystem processes and refine futurerestoration and management;• Public awareness and involvement in theTuolumne River restoration effort;• A clean river. Our perception of a river’sintrinsic value is largely based on visualaesthetics. To most people, a clean river isworth caring for, and the public will be moreconscious of keeping it clean.146

RESTORING THE TUOLUMNE RIVER CORRIDORThese restoration goals apply to all geomorphicreaches defined in Chapter 2. Because of land usedifferences among the seven different reaches,primary restoration issues differ between reaches.The following section presents specific restorationstrategies for each reach (Figure 4-1) that targetthese primary restoration issues.4.2 RESTORATION STRATEGIES4.2.1. Sand-Bedded Zone (San JoaquinRiver RM 0 to Fox Grove ParkRM 24)Primary restoration issues: Agricultural andurban encroachment of floodway, rip-rap levees,loss of riparian vegetation, loss of off-channelwetlands, loss of channel migration, poor waterquality, refuse.Overall restoration strategies for all sand-beddedreaches:• Improve salmon rearing capability by improvingwater quality through urban and agriculturalrunoff management programs, and byimproving water temperatures during rearingand outmigration periods;• Restore floodway capacity to 15,000 cfs orgreater above Dry Creek, and 20,000 cfs orgreater below Dry Creek;• Reduce permanent urban and agriculturalencroachment to create/maintain a 500-2,000 ftor greater floodway width;• Remove rip-rap and levees where feasible torestore a functional floodplain and naturalchannel migration within the floodway;• Improve water quality in Dry Creek;• Restore a continuous corridor of native riparianhardwoods;• Seek voluntary conservation easements and/orland acquisitions (especially of flood-pronelands) to increase riparian corridor width;• Remove exotic plants within riparian corridor.• Protect remaining mature valley oaks andFremont cottonwoods.4.2.2. Gravel-Bedded Zone (Fox GroveRM 24 to La Grange Dam RM52.1)Primary restoration issues: Agricultural encroachmentin floodway, historical instream andpresent-day off-channel gravel mining, rip-rapbank protection, dikes, dredger tailings, livestockgrazing, fine sediment accumulation, spawninggravel supply, moderate to poor salmon spawningand rearing habitat quality, riparian encroachmentalong the low flow channel.Overall restoration strategies for all gravelbeddedreaches:• Increase coarse sediment supply and maintaincoarse sediment budget;• Reduce fine sediment supply.• Restore floodway capacity to 15,000 cfs orgreater;• Reduce agricultural and mining encroachmentto create/maintain a 500 ft or greater floodwaywidth;• Remove rip-rap and levees where appropriate torestore a functional floodplain and allownatural channel migration within the floodway;• Manage flood control releases to increasefrequency of floods that exceed fluvial geomorphicthresholds (e.g., bed surface mobilization);• Provide variability in streamflows to increaseheterogeneity of physical habitat;• Restore a continuous corridor of native riparianhardwoods;• Revegetate restored floodplains and terraceswith native riparian plant assemblages;• Improve habitat quality of off-channel wetlands;• Seek voluntary conservation easements and/orland acquisitions (especially of flood-pronelands) to increase riparian corridor width;• Remove exotic plants from within the ripariancorridor;• Develop alternative grazing strategies toincrease natural riparian regeneration;• Protect existing mature valley oaks andFremont cottonwoods.CHAPTER 4147

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORSAND-BEDDED ZONE (RM 0.0 to RM 24.0)• Restore floodway capacity to 15,000 cfs or greater above Dry Creek and 20,000 cfs or greaterbelow Dry Creek• Reduce urban and agricultural encroachment to create/maintain a 500-2,000 ft or greaterfloodway width• Remove rip-rap and berms where feasible to restore floodplains and to allow migration withinthe floodway• Seek conservation easements and/or land acquisitions (especially of flood-prone lands) fromwilling landownersCHAPTER 4REACH 1 (RM 0.0-10.5)Lower Sand-bedded Reach• Restore off-channel wetlands toincrease wildlife habitat• Create vegetative buffer toreduce soil erosion and filteragricultural runoff• Restore functional floodplainsand native riparian forestsREACH 2(RM 10.5-19.3)Urban Sand-bedded Reach• Increase public awareness of theTuolumne and promote cleanup,restoration and monitoring• Improve Tuolumne RiverRegional Park by increasingarea of native riparian trees• Create and preserve riparianbuffer along urban/industrialzones• Remove trash and debris, eliminatechronic sources of pollution,and actively monitor illegaldumpingREACH 3(RM 19.3-24.0)Upper Sand-beddedReach• Preserve existingurban setback fromriver• Create andpreserve a riparianbuffer along urban/agricultural zonesREACH 4continuedFigure 4-1. Geomorphic reach delineation and proposed restoration strategies for the lower Tuolumne River.148

RESTORING THE TUOLUMNE RIVER CORRIDORGRAVEL-BEDDED ZONE (RM 24.0-52.1)• Increase gravel supply throughout the zone and increase the frequency of gravel movement• Reduce fine sediment supply and storage• Restore floodway capacity to 15,000 cfs or greater• Reduce agricultural and mining encroachment to create/maintain a 500 ft or greater coridor width• Remove rip-rap and berms where feasible to restore floodplains and to allow migration within thefloodway• Manage flood control releases to initiate bed movement and other dynamic channel processes• Restore a continuous corridor of native riparian vegetation• Improve habitat quality of off-channel wetlands• Seek conservation easements and/or land acquisitions (especially of flood-prone lands) fromwilling landowners• Remove exotic plants within riparian corridor and replant native species• Introduce alternative grazing strategies to promote riparian regenerationREACH 4(RM 24.0-34.2)In-Channel Gravel MiningReach• Isolate/fill instreammining pits to reducebass predation onjuvenile salmon andreestablish bedloadtransport continuity• Restore a natural river andfloodplain• Create and maintainriparian buffer (corridor)along urban/agriculturalzonesREACH 5(RM 34.2-40.3)Gravel Mining Reach• Isolate off-channelmining pits to preventriver connection duringfloods up to 15,000 cfs toreduce salmon strandingand bass predation onjuvenile salmon• Increase floodway widthto at least 500 feet• Restore a natural river andfloodplain morphology• Restore and maintainriparian corridor throughgravel mining zonesREACH 6(RM 40.3-46.6)Dredger Tailing Reach• Reconstruct remnantchannel left by golddredger operations to anatural river and floodplainform• Restore riffles to increasesalmon spawning andrearing habitat• Regrade floodplains toreduce salmon strandingand promote riparianregeneration• Reduce riparian encroachmentonto lowflow channel• Reduce grazing impactsto promote riparianregeneration• Secure remnant dredgertailings for futurerestorationREACH 7(RM 46.6-52.1)Dominant SpawningReach• Reduce sand input intoriver and storage inriverbed (especially inspawning gravels)• Increase and maintainspawning gravelsupply• Restore riffles toincrease salmonspawning and rearinghabitat• Regrade floodplains toreduce salmonstranding and promoteriparian regeneration• Reduce riparianencroachment ontoactive channel• Reduce grazingimpacts to promoteriparian regenerationon floodplainsCHAPTER 4149

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 44.3. RESTORATION ANDPRESERVATION APPROACHESSpecific approaches to achieve the above restorationvisions are discussed below.4.3.1. Preservation sitesPreserving the integrity of a site where humaninfluence has been minimal and ecologicalconditions have remained healthy should beprioritized equally with restoration sites. Preservingreaches that are functioning well today ismuch cheaper than restoring them tomorrow.Potential preservation sites can be moderatelydisturbed but must be easily restorable. Highpriority preservation sites should have:(1) high quality chinook salmon habitat, and/or(2) stands of Fremont cottonwood and valleyoak, and/or(3) a migrating channel creating diverse habitat(which is rare on the Tuolumne River).The highest priority site in the first category is theDominant Spawning Reach (Reach 7 in Figure 4-1) from Old La Grange Bridge (RM 50.5)downstream to the New Basso Bridge (RM 47.6).This reach is often heavily grazed, with livestockoften walking through spawning riffles duringand after spawning. The dredger tailings havebeen removed, leaving an unconfined floodplainsurface that offers considerable potential forriparian revegetation and channel migration. Thesecond priority site is the Dredger Tailing Reach(Reach 6 in Figure 4-1), which also has importantspawning habitat, sometimes heavy grazing, andfew remaining dredger tailings. The DredgerTailing Reach, with large stands of maturecottonwoods and a wide floodway, has the bestpotential for riparian forest restoration in theentire gravel-bedded reach. However, damage tothe channel by gold dredging must be remediedbefore expecting significant improvement insalmon spawning and rearing habitat.Reaches on the Tuolumne River where thechannel is migrating, creating alternate bars, andconstructing contemporary floodplains are rare inthe gravel-bedded zone, but less so in the sandbeddedzone. Their rarity in the gravel-beddedzone and their importance to salmon habitatrequires that these sites in the gravel-bedded zonereceive higher priority. Two examples are: (1)immediately upstream of the Roberts FerryBridge, where the channel is migrating intodredger tailings (RM 40.3), and (2) at RM 34.3where the channel is migrating into an oldfloodplain on the south bank. Bank erosion issupplying gravel and cobbles to the river channel;dynamic bars are forming immediately downstream,providing high-quality salmon habitat.Wherever possible, sites with a migrating channelshould be preserved, preferably with a purchase oreasement.4.3.2. Floodway expansionAs illustrated by the January 1997 flood (seeSection 3.1.6), adequate floodway capacity andfunctional floodplains are crucial to a healthyriver corridor. Many reaches have thin topsoil orgravel dikes that confine the river between deeppits, particularly in aggregate extraction areas. Inseveral areas the entire floodway width is asnarrow as 125 feet. Dikes are particularly proneto failure at moderate flood flows as low as 8,000cfs. When dikes fail, the river “captures” theentire floodplain gravel pit, and the pit remainsconnected to the main channel. Additionally,confinement by the dikes does not allow streamenergy to naturally dissipate on floodplains andriparian vegetation, but instead redirects theriver’s energy against the bed surface, degradingthe channel. Highly confined reaches (e.g.,downstream of Basso Bridge due to riparianencroachment, and within the Gravel MiningReach due to confining dikes) have become long,deep pools, with few, if any, riffles or otherinstream alluvial deposits. Alluvial deposits havebeen scoured away over time, as shown in Figures3-21 and 3-22.The ecologically and hydraulically preferablesolution is to increase the floodway width byeither moving dikes back from the channel(Figure 4-2) or by selectively removing riparian,agricultural, or dredger tailing confinement(Figure 4-3). Floodplains reconstructed to conveyhigh flows from 4,500 up to 15,000 cfs upstreamof Dry Creek (RM 16.4), and up to 20,000 cfsdownstream of Dry Creek, will greatly improvefloodway capacity and NDPP operational flexibility,thus greatly reducing the risk of futurecatastrophic floods. Restoring floodplains and ameandering channel will increase energy dissipationby creating bar features and encouragingriparian vegetation, rather than downcutting thechannelbed and eroding dikes (Figure 4-4).150

RESTORING THE TUOLUMNE RIVER CORRIDORFloodway width of at least 500 ft in the gravelbeddedzone is recommended for the followingreasons:• In reaches with minor or no channel damageduring the January 1997 flood, the minimumfloodway width was 500 ft.• Most bridge crossings and hard infrastructureconstraints can be avoided by a 500 ft widefloodway.• A 500 ft wide floodway will increase floodplainstorage of high flows, helping attenuate shortduration peak flows.• A riparian corridor can have several maturecottonwoods or valley oaks on each side of a200 ft wide bankfull channel, capable ofcreating a continuous corridor on both sides ofthe river with a closed canopy and associatedterrestrial habitat.• A 500 ft wide floodway provides room for thechannel to migrate in the future (migratethrough a floodplain or terrace rather thanthrough dikes).A 500 ft wide floodway also conveys a maximumdesired flood control release of 15,000 cfs. TheNDPP outlet works capacity is 14,500 cfs, andadded to 500 cfs of downstream flow accretionduring a storm event, results in a desired floodwaycapacity of 15,000 cfs upstream of DryCreek. Flow capacity was computed in a 500 ftwide channel (Figure 4-5), using the followingassumptions:1. Energy slope = 0.0015 based on 5400 cfswater surface slope measured at manylocations in the gravel-bedded zone in thespring of 1996;2. Manning’s n = 0.028 over entire channelimmediately after construction (smoothestchannel conditions) based on HEC-RASback-calculations of the 5,400 cfs flowmeasured in the spring of 1996;3. Manning’s n = 0.035 within the bankfullchannel and n = 0.075 on floodplain/terracesurfaces after vegetation has established andbegun to mature (roughest channel conditions);4. At least 3 feet of freeboard above watersurface required for dike stability.Results suggest that a 20,000 cfs flood could beconveyed with 6 feet of freeboard immediatelyafter construction, and 4 to 5 feet of freeboardafter riparian vegetation establishment roughenedthe channel (Figure 4-5). The 20,000 cfs valuewas used as a conservative discharge. Bothroughness scenarios pass the “safe” test with thesame safety factor (2 to 3 feet). For the rougherchannel condition, average channel velocitieswere 5.5 to 6.0 ft/sec, floodplain velocities wereapproximately 2 ft/sec, and main channel velocitieswere 7.5 to 8.0 ft/sec. This simple calculation,however, does not account for reaches with lowerslope, non-uniform flow, and increased roughnessfrom bars and channel curvature. Each channelrestoration project should evaluate floodway widthneeds using an appropriate hydraulic model (e.g.,HEC-RAS).4.3.3. Riparian restoration strategiesRiparian revegetation must be compatible withrestored hydrologic and fluvial processes. Asshown in Chapter 3, riparian plant species haveadapted to specific geomorphic surfaces that areinundated by specific flood recurrence intervals.General riparian restoration strategies shouldtarget Fremont cottonwood and valley oak as thehighest priority species due to their historic roleas dominant canopy structure and their subsequentdemise over time. Riparian restorationstrategies include:• plant cottonwoods on floodplain surfaces;• plant valley oaks on floodplain and terracesurfaces;• integrate revegetation with channel restorationwherever possible (e.g., use narrow-leaf willowbioengineering on outsides of meanders whereconstraints prohibit migration);• construct topographic depressions on floodplainsurfaces to create moist seedbeds that willencourage natural riparian regeneration;• revegetate restored floodplains and terraces inthe gravel-bedded zones in patches rather thanrigid grid spacing, preferably followingconstructed topographical depressions (seeFigures 2-19 and 2-38). This mimics thenatural patchiness of historic riparian forests inthe gravel-bedded zone, creating interiorhabitat for wildlife, creating perching androosting canopy structure, and providing aclosed canopy;CHAPTER 4151

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR130Left bank looking downstreamRight bankRelative Elevation (ft)125120115110105100Construct floodplain, revegetate withcottonwoods and valley oaksRevegetate toe of berm witharroyo willow (shrub)FillBermCutPre-construction Ground SurfaceDesign Ground SurfacePre-construction Low-flow Water Surface5,400 cfs Pre-construction Water Surface5,400 cfs Post-construction Water SurfacePre-construction Pond SurfacePost-construction Pond surface9590MiningPitFill85-400 -350 -300 -250 -200 -150 -100 -50 0 50 100 150 200 250 300 350 400Distance from Left Bank Pin (ft)Figure 4-2. Proposed modification to berm confined channel morphology to improve flood conveyance and reducehabitat damage during large floods.120115Left bank lookingdownstreamRight bankCHAPTER 4Relative Elevation (ft)1101051009590TerracesFloodplainCutFloodplainTerraces85Pre Construction Ground SurfaceDesign Ground SurfaceFill invert to reverse years ofPre-construction Low-flow Water Surface80channel downcutting5,400 cfs Pre-construction Water Surface5,400 cfs Post-Construction Water Surface75-50 50 150 250 350 450 550 650 750 850 950 1050 1150 1250Distance From Left Bank Pin (ft)Figure 4-3. Proposed modification to riparian and/or agriculturally encroached channel morphology to improve floodconveyance and reduce habitat damage during large floods.152

RESTORING THE TUOLUMNE RIVER CORRIDORFlowFlowLow flow channel - Run orlong poolBermsPonds or agriculturalRevegRevegetatedfloodplainsPool PoolRifflePointbarRifflePointbarPoolLow flowPointbarRevegetatedfloodplainsFloodwayEXISTING CONDITIONSBankfullFloodwayRESTORED CONDITIONSCHAPTER 4Figure 4-4. Recommended restoration strategy for straight reaches, converting incised channel to natural alternate barsequence with two stage channel. Note: Alternate bar morphology is idealized; designed conditions should be morevariable. Suggested dimensions are listed in Section 4.3.4 of the report.• revegetate restored floodplains and terraces inthe sand-bedded zone completely (as opposed topatches) using conventional farming techniques.Vegetation should be planted instaggered rows or in pseudo-sine waves,mimicking the natural spatial variability andachieving complete vegetation coverage.Complete planting coverage will become densegallery forests (much like Figure 2-17 and 2-27) and will provide interior forest habitatessential to wildlife (e.g., yellow billed cuckoo);• revegetate by series rather than species toprovide both the canopy species and understoryspecies;• actively remove confining riparian berms aspart of restoration projects in areas wherevegetative encroachment has occurred into theactive channel;• protect all restoration and preservation sitesfrom future disturbance through conservationeasements or land purchases.153

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORFigure 4-5. Conceptual restored floodway, with bankfull channel, floodplain, and terraces.CHAPTER 44.3.4. Channel reconstructionChannel reconstruction must incorporate dynamicfluvial geomorphic processes and a variablehydrologic regime in the design. Bed mobilizationand channel migration should be accommodatedand encouraged. Floodplains should be constructedto encourage fine sediment deposition ontheir surfaces. Designing channel restorationprojects within this dynamic framework willallow the river channel to naturally form andmaintain diverse habitat. A migrating channelwith an alternate bar morphology increasestopographic complexity. The ensuing hydrauliccomplexity generates a complex channelbed(Attribute #1) exhibiting a diverse particle sizedistribution. All physical adjustments combine tosustain complex habitat for many species.Moderate channel self-adjustment, therefore,should be considered a key characteristic for asuccessful restoration project.As discussed above, the minimum floodway widthshould be no less than 500 ft, and considerablywider as valley confinement ends downstream ofModesto. This channel design considerationdepends on the high flow regime. A largerfloodway width is needed downstream of DryCreek to accommodate larger flood controlreleases and tributary accretion. The floodwayserves environmental benefits along the TuolumneRiver corridor (riparian and channelrestoration) as well as improves operationalflexibility of the NDPP flood management system.Primary channel design parameters, includingbankfull channel width, depth, meander wavelength,radius of curvature, and sinuosity (dependentvariables), are tailored to more common“channel maintaining” floods, channel slope, andparticle size (independent variables). All thesevariables have some degree of interdependence,and at times, can all be unknown. The first step isto fix the primary independent variable: thechannel maintaining flow. We use bankfulldischarge as a surrogate for the channel maintainingflow, which is a primary variable for determiningchannel dimensions. Bankfull discharge istypically within the 1.5 to 2.5 year flood recurrence,and has decreased over the years with eachnew dam on the Tuolumne River. Using the post-NDPP high flow regime, the 1.5 and 2.5 yearfloods are 2,600 cfs and 4,400 cfs, respectively.The maximum release from which NDPP cangenerate power is approximately 5,500 cfs. Manypast floods have peaked between 5,000 cfs and5,500 cfs. If flood control modifications areimplemented as recommended in Section 3.2.2,the 1.5 and 2.5 year flood would only increase to2,700 and 5,000 cfs, respectively. The congruityof 5,000 cfs dam releases with bed mobilityobservations at the M.J. Ruddy restoration siteindicates that a target future bankfull dischargebe approximately 5,000 cfs.154

RESTORING THE TUOLUMNE RIVER CORRIDORObservations at the M.J. Ruddy 4-Pumps restorationproject, measurements at model reaches, andregional relationships of bankfull discharge tochannel dimension, resulted in the followingchannel design guidelines for restoratiionprojects in the gravel bedded reach:channel width at low water (~150 cfs) 75 - 90 feetthalweg depth at low water (pools) 4 - 8 feetthalweg depth at low water (riffles) 0.5 - 1.5 feetwidth at spawning flow (300-500 cfs) 90 - 110 feetaverage thalweg depth at spawningflow (riffles)1 - 2 feetaverage water velocity at spawningflow1.3 - 2.5 feet/secbankfull discharge5,000 cfsbankfull width175-200 feetaverage bankfull depth6 feetaverage bankfull water velocity4 - 5 feet/secmax floodway width, includingfloodplains & terraces>500 feetmaximum design floodway discharge 15,000 to 20,000 cfsmeander wavelength1,600 - 2,000 feetsinuosity 1.1 - 1.2radius of curvaturelargehigh flow energy slope 0.001 to 0.002These criteria were developed for the gravelbedded zone where bankfull slopes are between0.001 and 0.002. Further consideration would beneeded to develop similar design criteria for thesand-bedded zone, but channel reconstruction inthe sand-bedded zone should be minimal, otherthan for reshaping floodplains for riparianrestoration projects. The flood frequency distributionis also different below Dry Creek due tocumulative unregulated storm runoff fromtributaries.4.3.5. Fine sediment (sand)managementThe objective of fine sediment management is toreduce fine sediment storage within the bankfullchannel. To reduce fine sediment storage, eachvariable in the sediment budget equation “Input –Output = DStorage” must be targeted, including:• Reduce Input. Construct sedimentation ponds intributaries that deliver fine sediment to theTuolumne River; improve land use practiceswithin the corridor to reduce soil erosion anddelivery to the Tuolumne River.• Increase Output. Increase the magnitude andfrequency of high flows to deposit fine sedimentonto the floodplain; increase the magnitude,frequency and duration of high flows to scour,mobilize, and transport fine sediment downstreamfrom primary spawning and rearingreaches.• Mechanically reduce Storage. If above twomethods do not sufficently reduce instreamstorage, excavate sand stored in pools, excavatesand from riparian berms and backwaters,excavate sand on Basso area floodplains thathas high risk of returning to the river, andevaluate techniques to mechanically flush andremove sand from riffles. If fine sediment inputis sufficiently reduced, mechanical removalwould soon no longer be needed.4.3.6. Coarse sediment (spawninggravel) managementA discussed in Chapter 2, dams on the TuolumneRiver have trapped all coarse sediment derivedfrom the upper watershed, preventing downstreamreaches from being replenished. High flowevents and instream aggregate extraction haveprogressively reduced coarse sediment supplywithin the bankfull channel. Coarse sedimentincludes gravels and cobbles which form highquality salmon habitat. The objective of coarsesediment management is to first reverse historiclosses with a “transfusion,” of large volumes ofcoarse sediment, then maintain coarse sedimentstorage by periodically adding coarse sediment ata rate equal to the volume transported downstreamby high flows. Coarse sediment introductionshould first target the dominant spawningreach between La Grange Dam (RM 52.2) andBasso Bridge (RM 47.6) so that coarse sedimentcan then be routed downstream over time.Introducing coarse sediment as instream pointbars and pool tails restores and replenisheshabitat for immediate use by salmon (Figure 4-6).Later introductions should also occur downstreamof the dominant spawning reach, particularly afterrestoration of bedload impedance reaches and theGravel Mining Reach. Introduced coarse sedimentshould consist of gravel and cobble sizeCHAPTER 4155

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORclasses only, from approximately 8 mm (1/4 in)diameter to 128 mm (6 in) diameter. These sizeclasses are most useful to salmon, and are smallenough to be mobilized by the contemporary highflow regime.Coarse sediment is also naturally recruited fromchannel migration (bank erosion), so channelmigration should be allowed to occur whereverpossible. However, as channels migrate, thereneeds to be coarse sediment replenishment fromupstream sources to rebuild point bars on theinside of bends. Channel migration does notnecessarily provide a net input of coarse sedimentwhen it occurs, but is a mechanism for sedimentstorage and routing. Maintaining coarse sedimentsupply in upstream reaches of the TuolumneRiver is therefore necessary. Tributary contributionsof coarse sediment is also negligible. Thenext priority is then filling bedload impedancereaches (see Section 3.1.1) that trap coarsesediments in transport. Restoring these reaches toa morphology properly sized to the contemporaryhigh flow regime will allow coarse sediment fromupstream sources to continue the depositionmobilization-redepositionprocess that “recycles”introduced gravel year after year. Severalconceptual restoration designs developed by theRestoration Plan target these impedance reaches.4.3.7. Microhabitat restorationMicrohabitat restoration on a river the size of theTuolumne River is typically a short-term strategyat best, because periodic high flows still occurwith the capacity to destroy the restoration effort.Typical microhabitat restoration includes replacingsubstrate in riffles with clean gravel, constructingboulder weir grade control structures,placing boulder clusters for instream habitat, andmechanical gravel flushing. Most microhabitatrestoration projects have had limited success (e.g.,Kondolf et al. 1996), and should only be implementedif project benefits outweigh the costs of ashort project life-span.Mechanical gravel flushing may be a feasibleshort-term strategy for reducing fine sediment inCHAPTER 4Figure 4-6. Suggested “gravel transfusion” insertion method to quickly restore and replenish instream alluvial deposits.156

RESTORING THE TUOLUMNE RIVER CORRIDORspawning gravels, and if implemented, shouldinitially target the dominant spawning reachupstream of Riffle 5B (RM 47.9) under thefollowing conditions:• A solution to reduce fine sediment input fromGasburg Creek is implemented;• Sand deposited on floodplain surfaces from the1997 flood is removed and/or used to filldredger pits on floodplains.The longevity of the flushing effort must beincreased by removing upstream sand sources tomake mechanical sand flushing cost-effective.Sand sources downstream of Riffle 5B (e.g.,Lower Dominici Creek and Peaslee Creek) will bemore difficult to control; rapid sand infiltrationwill most likely shorten mechanical flushingeffectiveness.4.3.8 MiscellaneousThe TRTAC should consider identifying anappropriate site and installing an adult salmoncounting station. While not specifically a restorationactivity, a counting station would providemore accurate escapement estimates, and providevaluable information on migration timing. Thesecounts could also augment/validate the spawningsurvey data collected by CDFG in the spawningreaches. Finally, a fish trapping station could beused to capture hatchery fish or out-of-basinstrays and remove them from the Tuolumne Riverbreeding population, thus protecting the geneticdistinction of the Tuolumne River salmon, asmandated by the Settlement Agreement.4.4. RESTORATION SITEIDENTIFICATION ANDSELECTIONMany of the restoration projects identified by thisplan are of much larger scale than has recentlyoccurred, with project boundaries spanning theentire corridor width over several miles ofchannel length. We identified projects through acombination of discussions with local stakeholdersand scientists, restoration site lists developedby others (EA Engineering, DWR, CDFG), andan extensive re-evaluation during numerous floattrips and site visits. Restoration sites were eitherclassified as a channel restoration project orriparian restoration project; however, mostchannel restoration projects contained a strongriparian component, whereas riparian projectswere solely riparian.The logical progression from identifyingrestoration projects to implementing restorationprojects requires some prioritization toensure that the most important projects areimplemented first. Factors that limit salmonproductivity and the fundamental fluvialprocesses that make the system functionproperly should logically be addressed first,then factors that are less imperative, and so on.The task of prioritizing and selecting projects forimplementation is beyond the scope of thisdocument, but is the ultimate responsibility of theTuolumne River Technical Advisory Committee.Priorities may be adjusted over time as projectsare implemented and monitoring data can be usedadaptively to re-evaluate project success andenvironmental responses to restoration actions.The criteria for selecting projects may also varydepending on the availability of funding and thetype of funding source, opportunity (e.g., willinglandowner), the types of projects that wereimplemented previously, and other unforeseeablecircumstances. For example, several large-scalechannel reconstruction projects have alreadyreceived funding, and project implementation willbegin in 2000. The TRTAC may choose toevaluate the performance of these relativelyexpensive projects before proceeding withadditional channel reconstruction projects. Also,many of the riparian restoration projects dependon land purchases or conservation easements,both circumstances of which require willinglandowners before these projects can proceed. Thelogical way to proceed, therefore, is for theTRTAC to remain opportunistic in the face ofshifting availability of funding or land availability.In the interim, funding proposals weredeveloped for fourteen channel restorationprojects tentatively identified as high priority.These proposals are immediately available shouldthe appropriate implementation opportunity arise.CHAPTER 4157

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 4Conceptual designs were developed for thefollowing restoration projects, and summaries ofthe project background, objectives, projectdescriptions, and estimated costs are providedbelow:1. Special Run Pool 5 (RM 32.9 to 33.4)2. Special Run Pool 6 (RM 30.2 to 30.9)3. Special Run Pool 9 (RM 25.6 to 25.9)4. Special Run Pool 10 (RM 25.2 to 25.6)5. Gravel Mining Reach Phase I (RM 37.7 to40.3)6. Gravel Mining Reach Phase II (RM 36.6 to37.7)7. Gravel Mining Reach Phase III (RM 35.2 to36.6)8. Gravel Mining Reach Phase IV (RM 34.3 to35.2)9. Sediment Management and ImplementationPlan10. Gasburg Creek Sedimentation Basin (RM50.4)11. Dredger Tailing Reach Phase I (RM 45.4 to46.5)12. Dredger Tailing Reach Phase II (RM 43.8 to45.4)13. Dredger Tailing Reach Phase III (RM 42.2 to43.8)14. Basso Spawning Reach Floodplain Restoration(RM 47.6 to 50.5)Several projects that were not included in the listof 14 channel restoration projects deserveadditional discussion. First, the bedload impedancereach between Riffle 5B (RM 47.9) and thelate Riffle 6 (RM 47.0) presently preventssediment transport through it, and will continueto do so in the future. Gravel introduced as part ofthe sediment management program will becomedeposited here and not route downstream toreplenish the dredger tailing reach until thisbedload impedance reach is fixed. Channelrestoration and/or gravel additions in the dredgertailing reach will restore a large source of gravelfor downstream movement, but over the longtermwill be depleted until this impedance reachis filled. Any property in the dredger tailing reachthat becomes available for fee title purchase orconservation easement should be pursued. Thisreach has substantial salmon and riparianproduction presently, and there is considerablepotential to improve conditions in this reach.River front properties and those containing gravelsources should be prioritized for preservation andrestoration or material sources, respectively.The remaining two projects are SRP 7 (RM 26.0 to27.8) and SRP 8 (RM 27.9 to 29.5), which areextremely large remnant instream aggregateextraction pits. The cost to restore these pits islarge (over $5 million each). Restoration of twosimilar sites (SRP 9 and 10) are underway, andwe recommend that their effectiveness be evaluatedbefore proceeding with additional pit fillingprojects in the future to determine their costeffectiveness.These three projects should befurther developed in the near future within anexpanded list of projects.An additional three projects that are currentlybeing developed also warrant discussion. The“Grayson River Ranch Project” is a 140 acrefloodplain parcel on the south bank of theTuolumne River between river miles 5 and 6. Theproperty owners applied for and received a“perpetual conservation easement” for theirproperty in response to the 1997 flood andfrequent past flooding. The USDA NaturalResources Conservation Service administerseasement agreements in cooperation with the EastStanislaus County Resource ConservationDistrict, linking with various local, state, federal,and non-profit partners for funding and restorationcoordination.In the upper river, the “Bobcat Flat Project”involves the potential acquisition of a 280 acreparcel. The project involves the fee acquisition ofa large floodplain with two miles of river frontagein the dredger tailing reach. It has significantpotential for enhanced natural floodplain function.The proposal was submitted by the Friendsof the Tuolumne, and funding for the purchaseand restoration has been approved by CALFED.Finally, the City of Modesto has begun developmentand implementation of the “Tuolumne RiverRegional Parkway”, centered in the City ofModesto. This project includes revision of theJoint Powers Authority General Plan, developmentof the Gateway Parcel located downtown Modestonear the Ninth St. Bridge, and potentially extensiverestoration of riparian zones.158

RESTORING THE TUOLUMNE RIVER CORRIDOR4.5. SUMMARY OF 14 CHANNELRESTORATION PROJECTS4.5.1. Special Run Pool 5 ChannelRestoration ProjectBackgroundSRP 5 is a remnant instream aggregate extractionarea. Prior to aggregate extraction, this site wasdominated by a large right bank point bar withdiverse riparian vegetation. The point bar wasexcavated to a depth of 8-10 ft below the lowwater surface. Presently, the bedload supply toSRP 5 is from local erosion of the bed and banks,and supply is very small. Restoring SRP 5 inconjunction with upstream projects will restorebedload transport continuity from RM 40.3downstream to SRP 6 at RM 30.6 (more than30% of the gravel-bedded reach). Bedload canthen be used by the river to build and maintaindynamic gravel bars (available for chinookhabitat) rather than filling old pits. Restoring SRP5 is thus an important link to re-establishingfluvial processes in the gravel-bedded reaches ofthe Tuolumne River.Additionally, SRP’s limit chinook salmon survivalbecause the unnaturally wide channel and deepwater conditions offer suitable habitat to nonnativelargemouth and smallmouth bass, and thenative Sacramento squawfish, all of which preyon juvenile chinook salmon. Because a majorityof chinook spawning in the Tuolumne Riveroccurs upstream of this location, most juvenilesmust pass through this reach. Reducing predationshould therefore increase Tuolumne River smoltproduction.Project ObjectivesSpecial Run-Pool 5 (SRP 5) is located approximately17 miles east of Modesto and extends fromRM 32.9 to 33.4. The project will restore a twostagechannel morphology scaled to the presentand future flow regime, facilitate sedimenttransport and routing, restore chinook salmonhabitat, and increase riparian vegetation. Specificobjectives of the project are:• Reduce/eliminate habitat favored by predatorybass species, and replace with high qualitychinook salmon habitat.• Restore channel and planform morphologyscaled to contemporary and future sediment andhydrologic regimes.• Restore sediment transport continuity andeliminate bedload impedance reaches.• Revegetate reconstructed floodplains andterraces with native woody riparian species,planted on surfaces designed to inundate atdischarges appropriate for each species/serieslife cycles.• Link restored reaches upstream (Reed site;Gravel Mining Reach) with planned restorationactivities downstream (SRP 6) to restoreecological and geomorphological connectivityto reaches containing important chinooksalmon habitat.Project DescriptionThe project will reverse the impact of instreammining by filling the instream pit and restoringan alternate bar sequence through the reach,requiring approximately 175,000 yd 3 of fillmaterial. SRP 5 is located where the valley wallsnaturally confine the floodway to less than 550 ftwide. Since the valley walls are essentially nonerodible,bank protection is unnecessary. Ameander bend will be located against the northernbluff, with a 20 to 30 foot floodplain buffer toallow the channel space to migrate. The designattempts to minimize fill by retaining 8 footdepths to the pools, and restoring only one valleyoak terrace. Aggregate should be used to rebuildmost of the channel (108,000 yd 3 ), but topsoil/wash material will be used for floodplain andterrace surfaces (67,000 yd 3 ).The proposed design will also re-establish plantseries patterns identified during the riparianinventory, including willow and alder stands,Fremont cottonwood, and valley oaks, planted onsurfaces successively distant and at higherelevations, respectively, relative to the low waterchannel. Floodplains should be designed toinundate at approximately the post-NDPP 1.5 to2.5-yr flood frequency. Cluster planting willcreate a more natural look to the site, easewatering and maintenance, and increase habitatdiversity. Irrigation will be required for twosummers. Revegetation materials will comeeither from on-site sources (valley oak seeds,willow cuttings, cottonwood cuttings), or fromlocal nurseries (sedges, alder, and Oregon ash).CHAPTER 4159

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 4Fluvial geomorphic, riparian and biologicalobjectives of the project will be monitored toassure project performance success. The totalestimated cost for SRP 5 implementation is$1,463,000.For additional details, the complete projectconceptual design is available upon request.4.5.2. Special Run Pool 6 ChannelRestoration ProjectBackgroundSRP 6 is a remnant instream aggregate extractionarea. Prior to aggregate extraction, the channelhad low sinuosity with well vegetated alternatebar sequences. The low water channel was locatedat the base of bluffs along the north bank, with alarge floodplain on the south bank. Aggregateextraction started in the center of the channel andgradually expanded, widening and deepening thechannel to its present state. The primary bedloadsupply to SRP 6 is from erosion of an unminedgravel bar upstream, and supply is very small.Restoring SRP 6 in conjunction with upstreamprojects (SRP 5; Reed site; Gravel Mining Reach)will restore bedload transport continuity from RM40.3 downstream to SRP 7 at RM 29.6. Bedloadcan then be used by the river to build and maintaindynamic gravel bars (available for chinookhabitat) rather than filling old pits. Restoring SRP6 is thus an important link to re-establishingalluvial processes in the gravel-bedded reaches ofthe Tuolumne River.Additionally, SRP’s limit chinook salmon survivalbecause the unnaturally wide channel and deepwater conditions offer suitable habitat to nonnativelargemouth and smallmouth bass, and thenative Sacramento squawfish, all of which preyon juvenile chinook salmon. Because a majorityof chinook spawning in the Tuolumne Riveroccurs upstream of this location, most juvenilesmust pass through this reach. Reducing predationshould therefore increase Tuolumne River smoltproduction.Project ObjectivesSpecial Run-Pool 6 (SRP 6) is located approximately14 miles east of Modesto and extends fromRM 30.2 to 30.9. The project will restore a twostagechannel morphology scaled to the presentand future flow regime, facilitate sedimenttransport and routing, restore chinook salmonhabitat, and increase riparian vegetation. Specificobjectives of the project are:• Reduce/eliminate habitat favored by predatorybass species, and replace with high qualitychinook salmon habitat.• Restore channel and planform morphologyscaled to contemporary and future sediment andhydrologic regimes.• Restore sediment transport continuity andeliminate bedload impedance reaches.• Revegetate reconstructed floodplains andterraces with native woody riparian species,planted on surfaces designed to inundate atdischarges appropriate for each species/serieslife cycles.• Link restored reaches upstream with plannedrestoration activities downstream to restoreecological and geomorphological connectivityto reaches containing important chinooksalmon habitat.Project DescriptionThis project will fill the large aggregate extractionpits and establish a 500 ft wide floodway thatconveys flows of at least 15,000 cfs. A meanderingalternate bar morphology will be re-establishedthrough SRP 6. Two fields located on theright bank were incorporated into the project.These historic floodplain surfaces will be loweredapproximately three feet to provide approximately60,000 yd 3 of fill, decreasing the volume of offsiteaggregate needed. Lower design elevationswill also allow these floodplains to inundate atmore frequent flood recurrences. The remainingaggregate (159,000 yd 3 ) will likely be providedfrom off-site sources. Aggregate should be used torebuild most of the channel, but topsoil/washmaterial will be used for floodplain and terracesurfaces.The proposed design will also re-establish plantseries patterns identified during the riparianinventory, including willow and alder stands,Fremont cottonwood, and valley oaks, planted onsurfaces successively distant and at higherelevations, respectively, relative to the low waterchannel. Floodplains will be designed to inundateat approximately the post-regulated 1.5 to 2.5-yrflood. Cluster planting will create a more naturallook to the site, ease watering and maintenance,and increase habitat diversity. Irrigation will be160

RESTORING THE TUOLUMNE RIVER CORRIDORrequired for two summer seasons. Revegetationmaterials will come either from on-site sources(valley oak seeds, willow cuttings, cottonwoodcuttings), or from local nurseries (sedges, alder,and Oregon ash).Fluvial geomorphic, riparian and biologicalobjectives of the project will be monitored toassure project performance success. The totalestimated cost for SRP 6 implementation is$2,334,000.For additional details, the complete projectconceptual design is available upon request.4.5.3. Special Run Pool 9 ChannelRestoration ProjectBackgroundAt SRP 9, aggregate extraction created a 400 ftwide by 6 ft to 19 ft deep pit, and eliminatedfloodplains on the north and south banks (Figure4-6). Restoring SRP 9 in conjunction with SRP 10will restore bedload transport continuity throughthis reach, which can be used by the river to buildand maintain dynamic gravel bars (available forchinook habitat).SRPs 9 and 10 are the largest known predatorisolation projects on the Tuolumne River, andthus the most expensive to restore. SRP’s limitchinook salmon survival because the unnaturallywide channel and deep water conditions offersuitable habitat to non-native largemouth andsmallmouth bass, and the native Sacramentosquawfish, all of which prey on juvenile chinooksalmon. Because a majority of chinook spawningin the Tuolumne River occurs upstream of thislocation, most juveniles must pass through thisreach. Reducing predation should thereforeincrease Tuolumne River smolt production.Project ObjectivesSpecial Run-Pool 9 (SRP 9) is located immediatelydownstream of Fox Grove County Park, 10miles east of Modesto, and extends from RM 25.6to 25.9. Specific objectives of the project are:• Reduce/eliminate habitat favored by predatorybass species, and replace with high qualitychinook salmon habitat.• Restore channel and planform morphologyscaled to contemporary and future sediment andhydrologic regimes.• Restore sediment transport continuity andeliminate bedload impedance reaches.• Revegetate reconstructed floodplains andterraces with native woody riparian species,planted on surfaces designed to inundate atdischarges appropriate for each species/serieslife cycles.Project DescriptionThe proposed treatment is to fill most of the pit,and re-establish an alternate bar morphologythrough the reach. The upstream boundary of theSRP 9 pit (RM 25.9) is a riffle that will act as theproject entrance control, and will not be disturbedduring construction. The downstream boundary isthe riffle crest at the outlet of SRP 9. Modificationto the elevation of this outlet control will dependon the gradient through the reach. Restoring asingle thread channel and floodplain through theSRP 9 segment will require approximately146,000 yd 3 of fill material. Imported aggregate atthe SRP 9 site will fill the pool along the northand south banks to reclaim a floodplain. A poolrifflesequence will be constructed, and transitionto a riffle at the bottom of SRP 9. The low waterchannel width will be reduced to a maximum of100 ft.The proposed design will also re-establish plantseries patterns identified during the riparianinventory, including willow and alder stands,Fremont cottonwood, and valley oaks, planted onsurfaces successively distant and at higherelevations, respectively, relative to the low waterchannel. Floodplains will be designed to inundateat approximately the post-regulated 1.5 to 2.5-yrflood. Cluster planting will create a more naturallook to the site, ease watering and maintenance,and increase habitat diversity. Irrigation will berequired for two summer seasons. Revegetationmaterials will come either from on-site sources(valley oak seeds, willow cuttings, cottonwoodcuttings), or from local nurseries (sedges, alder,and Oregon ash).Some restoration activities are proposed for thesegment connecting SRP 9 and SRP 10, includingfilling four backwater areas with an additional 3,500yd 3 of fill material. The slope through this segmentmay also be redistributed downstream to increasethe gradient through SRP 9 and SRP 10. The sharpmeander 1,000 ft upstream of the head of the SPR10 pool (river turns south) is eroding into anCHAPTER 4161

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 4orchard, and this bend will be recontoured to amore gentle bed and revegetated to minimize futurebank erosion.Fluvial geomorphic, riparian and biologicalobjectives of the project will be monitored toassure project performance success. The totalestimated cost for SRP 9 implementation is$2,700,000.For additional details, the complete projectconceptual design is available upon request.4.5.4. Special Run Pool 10 ChannelRestoration ProjectBackgroundAt SRP 10 aggregate extraction created a 400 ftwide by 36 ft deep in-channel pit, and eliminatedthe large point bar and floodplains on the northbank (Figure 4-6). Restoring SRP 10 in conjunctionwith SRP 9 will restore bedload transportcontinuity through this reach, which can be usedby the river to build and maintain dynamic gravelbars (available for chinook habitat).SRPs 9 and 10 are the largest known predatorisolation projects on the Tuolumne River, andthus the most expensive to restore. SRP’s wereidentified as limiting factors to chinook salmonsurvival, because the unnaturally wide channeland deep water conditions offer suitable habitat tonon-native largemouth and smallmouth bass, andthe native Sacramento squawfish, all of whichprey on juvenile chinook salmon. Because amajority of chinook spawning in the TuolumneRiver occurs upstream of this location, mostjuveniles must pass through this reach. Reducingpredation should therefore increase TuolumneRiver smolt production.Project ObjectivesSpecial Run-Pool 10 (SRP 10) is located one miledownstream of Fox Grove County Park, 9 mileseast of Modesto, and extends from RM 25.2 to25.6. Specific objectives of the project are:• Reduce/eliminate habitat favored by predatorybass species, and replace with high qualitychinook salmon habitat.• Restore channel and planform morphologyscaled to contemporary and future sediment andhydrologic regimes.• Restore sediment transport continuity andeliminate bedload impedance reaches.• Revegetate reconstructed floodplains andterraces with native woody riparian species,planted on surfaces designed to inundate atdischarges appropriate for each species/serieslife cycles.Project DescriptionThe proposed treatment will fill most of the pit,and re-establish an alternate bar morphologythrough the reach. The project design is to fill thepool primarily from the north bank to createfloodplain and native riparian habitat. The lowwater channel in SRP 10 will be reduced to amaximum width of 100 ft, and will flow alongwhat is now the south bank. The 1997 floodcaused damage to the dike on the south bank onprivate property adjacent to SRP 10, and willrequire repair during the construction phase toensure project longevity. The outside of themeander (curving north) along the south bankwill be recontoured with a widened floodplain.The proposed channel topography will includethree pool /riffle sequences (max pool depth =10ft). SRP 10 will require 293,000 yd 3 of material,substantially more than SRP 9 because of thegreater pool depth.The proposed design will also re-establish plantseries patterns identified during the riparianinventory, including willow and alder stands,Fremont cottonwood, and valley oaks, planted onsurfaces successively distant and at higherelevations, respectively, relative to the low waterchannel. Floodplains will be designed to inundateat approximately the post-regulated 1.5 to 2.5-yrflood. Cluster planting will create a more naturallook to the site, ease watering and maintenance,and increase habitat diversity. Irrigation will berequired for two summer seasons. Revegetationmaterials will come either from on-site sources(valley oak seeds, willow cuttings, cottonwoodcuttings), or from local nurseries (sedges, alder,and Oregon ash).Fluvial geomorphic, riparian and biologicalobjectives of the project will be monitored toassure project performance success. The totalestimated cost for SRP 10 implementation is$4,657,000.For additional details, the complete projectconceptual design is available upon request.162

RESTORING THE TUOLUMNE RIVER CORRIDOR4.5.5. Gravel Mining Reach ChannelRestoration Project (Four phases)BackgroundImpetus for restoration in this reach comesprimarily from the extensive channel confinementand consequent channel degradation that isoccurring throughout this reach. Recurring failureof dikes separating off-channel aggregate extractionpits, accentuated by damage during the 1997flood has also contributed to degraded habitatconditions. The January 3 flood releases fromNew Don Pedro Reservoir and spillway peaked atnearly 60,000 cfs. Flood damage occurred notonly to the channel and dike system, but also tothe aggregate extraction operations, causingmillions of dollars in damage and lost revenue.Damage included multiple dike failures, completechannel capture through aggregate pits to thesouth of the 7/11 Aggregates plant, loss of theM.J. Ruddy conveyor bridge and Roberts FerryBridge, damage to plant operation structures, andsubstantial degradation to salmon habitat (loss ofriffles, channel downcutting and fine sedimentintroduction from the settling ponds). TheDistricts are requesting the US Army Corps ofEngineers to consider increasing the maximumallowable flood release from the present 9,000 cfsto at least 15,000 cfs at Modesto to improve floodcontrol. Substantial upgrades to dikes andincreased floodway capacity in this reach isessential.Project ObjectivesThe six mile long Gravel Mining Reach is locatednear Waterford, CA, between Roberts Ferry Roadat RM 40.3 and the downstream extent of thecontemporary aggregate extraction operations atthe George Reed site at RM 34.3. The projectreach is divided into four implementation phasesbased on property ownership boundaries. Multipleobjectives of the project include:• Restore a floodway width that will safelyconvey floods of at least 15,000 cfs.• Improve salmon spawning and rearing habitatsby restoring an alternate bar (pool-riffle)morphology, restoring spawning habitat withinthe meandering channel, and filling in-channelmining pits.• Prevent salmon mortality that results fromfrequent connection between the TuolumneRiver and off-channel mining pits.• Restore native riparian communities on appropriategeomorphic surfaces (i.e., active channel,floodplains, terraces) within the restoredfloodway.• Restore habitats for special status species (e.g.,egrets, ospreys, herons).• Allow the channel to migrate within therestored floodway to improve and maintainriparian and salmonid habitats.• Remove floodway “bottleneck” created byinadequate dikes (e.g., dike failure above acertain discharge threshold).• Protect aggregate extraction operations,bridges, and other human structures from futureflood damage.Project DescriptionThe proposed long-term solution is to restore ariparian floodway with a minimum width of 500ft to 600 ft to safely convey discharges of at least15,000 cfs with fully grown riparian vegetationand a reasonable safety factor. The projectproposes to revegetate floodplains with nativeriparian series, similar to the revegetation plansdescribed for the SRP projects. The 330 acres ofexisting ponded wetlands associated with the offchannelaggregate extraction pits will be reducedto 270 acres.Timeline: because of the large scale of the GravelMining Reach project, implementation will occurin four phases, and follow the tentativecompletion dates outlined below:• Phase I 7/11 segment to be completed in 2001• Phase II M.J. Ruddy segment to be completedin 2002• Phase III Deardorff segment to be completed in2003• Phase IV Reed segment to be completed in2004Phase I: 7/11 segmentThis segment is defined by the extent of 7/11aggregate extraction upstream of Roberts Ferrybridge (RM 40.3) downstream to the M.J. Ruddyproperty line below the 7/11 plant site (RM 37.7).Impacts of the 1997 flood included channel capturethrough aggregate ponds to the south of the 7/11plant site (RM 39.0 to RM 37.6), river capture of the7/11 settling pond near the haul road bridge (RMCHAPTER 4163

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 437.9), and damage to dikes upstream of the 7/11plant site (RM 38.1 to RM 38.6). For constructionof Phase I, a total of 420,000 yd 3 of off-site aggregatematerial will be imported. The material sourcesite is another 7/11 Materials site on the southbank upstream of Roberts Ferry Bridge. The sourceand construction sites are connected by offhighwayhaul roads associated with 7/11 Materialsaggregate operations, which run along the southbank. Maximum haul distance is 2.5 miles from thesource site to the downstream end of the 7/11segment. Phase I construction will decrease thechannel area within the normal high water boundaryof 5,400 cfs (Waters of the U.S. designation)from 84.5 acres to 74.9 acres. Approximately 114acres of floodplain will be created by moving dikes,importing materials and grading existing sites,increasing the total floodway width to a minimum500 ft, and flood capacity to convey at least15,000 cfs. Revegetation of floodplains willincrease native riparian habitat from 83.1 acres to101.1 acres. A total of 24.4 acres of nativevegetation (primarily narrow-leaf willow) will beremoved as part of channel relocation and/or toacquire revegetation materials; 1.1 acres of exoticvegetation will be removed.Phase II: M.J. Ruddy segmentThis segment is defined by the property lineupstream of Joe Ruddy’s orchard (RM 37.7)downstream to Santa Fe Aggregates haul roadbridge (RM 36.6). The 1997 flood cauksedextensive damage to the 4-Pumps restorationproject reach, connecting the river to south bankponds at RM 37.1, RM 36.6, and RM 36.2, andconnecting a north bank pond at RM 36.7.Construction in the M.J. Ruddy Phase II segmentwill require importing an estimated 465,000 yd 3of aggregate and topsoil material. Constructionwill decrease the channel area within the normalhigh water boundary of 5,400 cfs (Waters of theU.S. designation) from 38.7 acres to 32.0 ft.Approximately 36.4 acres of floodplain will becreated or modified to increase the floodwaycapacity, and native riparian habitat will beincreased from 18.6 acres to 42.2 acres. A total of1.6 acres of native vegetation (narrow-leafwillow) will be removed as part of channelrelocation and/or to acquire revegetationmaterials.Phase III: Warner/Deardorff segmentThe Warner/Deardorff segment is defined by theSanta Fe Aggregates haul road bridge (RM 36.6)downstream to the entrance to Dan Casey Slough(RM 35.2). Damage by the 1997 flood consistedof numerous dike failures on the south bankdownstream of the haul road bridge, destructionof Santa Fe Aggregates conveyor bridge, andconnection of the Tuolumne River to the TularePond at flows greater than 2,000 cfs. Constructionin this segment may require no material importation,but will relocate large volumes of on-sitematerials. Haul roads are available on both sidesof the river. Construction will increase thechannel area within the normal high waterboundary of 5,400 cfs (Waters of the U.S. designation)from 39.0 acres to 42.2 acres. This phasewill also create approximately 63.6 acres offloodplain. Native riparian vegetation willincrease from 56.9 acres to 67.5 acres. A total of9.0 acres of narrow-leaf willow will either bedisturbed or removed as part of channel relocationand/or to acquire revegetation materials.Phase IV: Reed segmentThe Reed segment is defined by the entrance toDan Casey Slough on the upstream end (RM35.2), and the upstream extent of the ReedMitigation restoration project on the downstreamend (RM 34.3). Damage during the 1997 floodwas limited to the upstream and downstream endsof the existing south bank pond at RM 34.5.Similar to the Tulare Pond excavation in phaseIII, the Reed segment restoration may excavatematerials purchased and available on-site for allchannel and floodplain reconstruction. Constructionwill increase the channel area within thenormal high water boundary of 5,400 cfs (Watersof the U.S. designation) from 22.7 acres to 25.4acres. Restoration will create approximately 48.2acres of floodplain. Native riparian vegetationwill be increased from 35.9 acres to 47.5 acres. Atotal of 2.9 acres of native vegetation (narrow-leafwillow) will be removed as part of channel relocationand/or to acquire revegetation materials.Fluvial geomorphic, riparian and biologicalobjectives of the project will be monitored toassure project performance success. The totalestimated cost for Gravel Mining Reach implementationis $23,669,000. Funding for Phases Iand II have been provided by USFWS-AFRP andCALFED; funding for Phases III and IV has not164

RESTORING THE TUOLUMNE RIVER CORRIDORyet been received, but project approval andfunding availability will likely affect the timelinefor completion of these phases.For additional details, the complete projectconceptual design is available upon request.4.5.6. Tuolumne River SedimentManagement and ImplementationPlanBackgroundConstruction of La Grange Dam in 1893 (RM52.0) permanently ended coarse sediment supplyto the Tuolumne River channel downstream of LaGrange Dam. Because the few small tributariesentering the Tuolumne River downstream of LaGrange contribute virtually no coarse sediment,coarse sediment available for downstreamtransport is currently limited to sediment stored incontemporary channel, floodplain, and terracedeposits, or bank erosion of dredger tailings. Inthe absence of an upstream source, high flowevents have selectively transported medium-sizedparticles (gravels) from the bed surface, removinggravel bars and leaving behind large cobbles andboulders that armor the bed surface layer. Additionally,fine sediment (sand and silt) input andstorage into the Tuolumne River has increased inrecent years, as a result of tributary inputs and theJanuary 1997 flood.Fine sediment stored in spawning gravels reducessurvival of salmonid embryos. Chinook salmondepend on an adequate quantity of high qualitycoarse sediment deposits for spawning andrearing, and require a significant portion of thesedeposits to be of gravel and small cobble sizeclasses with relatively low proportions of finesediment. The reduced quantity and quality ofspawning habitat has reduced the productivecapacity of Tuolumne River spawning reaches,and has concentrated chinook salmon in shortreached below La Grange Dam that contain therelatively highest quality spawning gravels.Actions to reverse past trends in sediment supplyimbalances by balancing coarse sediment supplyand downstream routing and reducing finesediment input have the potential to increasesalmon production in the Tuolumne River andachieve chinook salmon production targets set forthe Tuolumne River.Project ObjectivesThis sediment management plan presents fourobjectives:• increase coarse sediment storage in the channelwith a large “transfusion” of coarse sediment toprovide alluvial deposits immediately availablefor chinook salmon spawning, and for eventualdownstream transport and redeposition;• maintain this restored coarse sediment storageby periodic augmentation of coarse sedimentsupply equal to the rate of downstream sedimenttransport;• implement remedial actions to prevent furtherextensive fine sediment input into the TuolumneRiver from Gasburg Creek (located nearthe upstream end of the spawning reaches);• implement actions to reduce fine sedimentstorage in the mainstem Tuolumne River.Project DescriptionThe purpose of this project is to develop andimplement a comprehensive sediment managementplan for the gravel-bedded reaches of theTuolumne River to restore coarse sediment supplyand reduce fine sediment input into the river.Four crucial tasks for restoring and maintaining abalanced sediment budget are identified: Task 1will develop a sediment management andimplementation plan that includes design,implementation, adaptive management, and themonitoring required for adaptive management.Task 1 also includes refinement of a chinooksalmon juvenile production model developed bythe Districts that can be used to predict thebenefits of sediment management toward salmonproduction. Task 2 will continue a program ofcoarse sediment augmentation (begun by CDFG),including refinement of proposed introductionsites, introduction volumes, and monitoringprotocols. Task 3 will initiate a program for finesediment reduction, by: (1) reducing fine sedimentsupplied to the upper river from the Gasburg Creekwatershed, (2) evaluating alternative methods forfine sediment reduction/removal in the mainstemTuolumne River, and (3) implementing fine sedimentremoval from the mainstem channel. Task 4will develop an adaptive management and monitoringprogram for quantifying coarse sedimenttransport to provide volume estimates for annualaugmentation, to maintain coarse sediment storagein the mainstem channel.CHAPTER 4165

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 4The total cost for this project, including projectmanagement, planning, and implementation, is$414,500. Costs for future coarse sediment managementwill depend on the magnitude, frequency, andduration of gravel transporting high flow events.Replacing the quantity of gravel transported out ofthe gravel-bedded reaches would cost more duringwet years than during dry years years when flowsdo not transport appreciable quantities of coarsesediment, and gravel augmentation is not required.This proposal contains revised designs for aGasburg Creek Sedimentation Basin.For additional details, the complete projectconceptual design is available upon request.4.5.7. Dredger Tailing Reach ChannelRestoration Project (Threephases)BackgroundThe Dredger Tailing Reach restoration project islocated in the heart of the gravel-bedded zonebetween river miles (RM) 42.5 and 46.8 (Reach 6of the Restoration Plan). This reach was severelydegraded by gold dredgers in the early- to mid-1900s, and combined with flow and sedimentregulation, has not significantly recovered in thefollowing decades. The Dredger Tailing Reachcontains chinook salmon spawning riffles whichare degraded, of poor quality, and receive significantlyless spawning use than spawning areasfurther upstream. Within its current physicalconstraints, this reach cannot recover to adesirable state on its own, but offers real opportunityfor restoring natural channel and floodplainfeatures, chinook spawning and rearing habitats,and reducing predator populations.Project ObjectivesThe overall goal of this project is to convert afossilized, highly degraded, remnant channel backinto a dynamic meandering channel. Primaryobjectives include:• Rebuild a natural channel geometry scaled tocurrent channel-forming flows.• Allow the channel to migrate within therestored floodway to improve and maintainriparian and salmonid habitats.• Restore and increase salmon spawning andrearing habitats by restoring an alternate bar(pool-riffle) morphology, restoring spawninghabitat within the meandering channel.• Eliminate salmon stranding problems associatedwith backwaters and sloughs, and floodplain“traps” accessed during moderate flows.• Acquire adjacent floodplain properties fromvoluntary land owners, either through purchaseor conservation easements. The Bobcat FlatLand Acquisition currently being negotiated isan excellent example of the type of opportunityavailable within the Dredger Tailing Reach.• Restore native riparian communities onappropriate geomorphic surfaces (i.e., activechannel, floodplains, terraces) within therestored floodway.• Restore riparian canopy habitats for otherendemic wildlife species (e.g., egrets, ospreys,herons).Project DescriptionThe large size of this reach requires that implementationoccur in three phases, similar to projectphasing in the Gravel Mining Reach. The reacheswere delineated by unique restoration objectivesand sections of channel that will require little orno restoration (natural delineation breaks).Phase I: Zanker Reach (RM 45.4 to 46.5)The upstream portion of this reach is long andstraight, confined by encroached riparian vegetation(RM 46.0 to 46.5). Immediately downstream,the riparian vegetation is less confining and thevalley confinement decreases (RM 45.4 to RM46.0). During high flow events, the bed surface inthe confined section incises, with scouredmaterial depositing and aggrading where confinementceases. The result is a long deep chute-likereach upstream with functionally no alluvialdeposits, and an aggraded bar downstream thatbacks water upstream into a “lake.” The riffle isover-steepened to the point where preferablespawning depths and velocities are in the tail-outarea and the margins of the steep riffles. Proposedactivities in the unconfined section includingexcavating a large portion of the bar to restorenatural riffle gradient, using excavated materialsto build bankfull confinement locally and fillportions of the channel in the upstream section.166

RESTORING THE TUOLUMNE RIVER CORRIDORActivities in the upstream section may includefilling portions of the confined low flow channelto pre-flood elevations, removing selected portionsof the riparian berms to increase bankfull channelsinuosity, and constructing point bars oppositethose locations to further encourage sinuosity.Although some on-site construction materials areavailable, significant fill material may be need fromoff-site sources. Riparian revegetation will occurduring and after channel construction.Phase II: Peaslee Creek Reach (RM 43.8 to 45.4)The Peaslee Creek Reach is solely a remnant ofgold dredger activities and aggregate removal forconstructing the NDPP. The channel is often deepand multi-channeled, following a tortuous coursein the general downstream direction. Excavated“floodplain” surfaces are at reasonable post-NDPP floodplain elevations, but the “bankfull”channel is extremely wide due to the remnantdredger-created channel. Additionally, thedredger mining left extremely steep riffles thatprovide poor salmon spawning habitat. Proposedactivities include recreating a single thread lowflow and bankfull channel through the reach,redistributing channel gradient through the reachto restore low gradient riffles, increasing bankfullchannel sinuosity, restoring functional floodplains,and revegetating with native riparianvegetation. Salmon spawning habitat should begreatly increased by implementing this project.There is essentially no construction materials onsite,so material would have to be imported fromother sources.Phase III: Hall Reach (RM 42.2 to 43.8)The Hall Reach is very similar to the PeasleeCreek reach, with the exception of havingadequate construction materials in the form ofdredger tailings at RM 43. Proposed activitieswill again include recreating a single thread lowflow and bankfull channel through the reach,redistributing channel gradient through the reachto restore low gradient riffles, increasing bankfullchannel sinuosity, restoring functional floodplains,and revegetating with native riparianvegetation. Salmon spawning habitat will again begreatly increased by implementing this project.A cost for implementing this project has not beenestimated due to continuing TRTAC discussion onspecific restoration approaches, and evolvinglandowner interest in conservation easementsand/or fee-title purchases.For additional details, the complete projectconceptual design is available upon request.4.5.8. Basso Spawning Reach floodplainrestoration (RM 47.6 to 50.5)BackgroundA 60-year legacy of gold mining, grazing, anddam construction has resulted in fragmentedriparian stands, poor or non-existent valley oakand cottonwood regeneration, fossilized alluvialdeposits, remnant pits that periodically strandjuvenile chinook salmon during receding highflows, and reduced spawning gravel storagewithin the bankfull channel. Extensive golddredging (from valley wall to valley wall)occurred through the 1940’s, leaving no definedchannel, and voluminous dredger tailings piledon floodplain surfaces. Flood events after 1937began reinitiating a defined channel through thetailings, but by 1963 the channel still lackeddefined floodplains and meander sequences.These dredger tailings were removed for theconstruction of New Don Pedro Dam from 1965to 1970. Their removal left shallow pits and nondrainingsurfaces. After New Don Pedro Dam wascompleted in 1971, the channel between rivermile 50.5 and 46.6 was reconstructed to improvechinook salmon spawning habitat. However,riparian vegetation and floodplains were notrestored, and cattle grazing and flow regulationhas discouraged riparian regeneration at the site.White alder and narrow-leaf willow have encroachedonto point bars, partially fossilizingthese alluvial deposits. Lastly, the 1997 flooddeposited tens of thousands of cubic yards of sandin the reach. The interaction between floodplainelevation, riparian vegetation and a contemporarybankfull discharge must be restored.The cumulative impacts of these changes tochinook salmon habitat has been amplifiedbecause this reach has the highest concentrationof spawning in the river, and possibly the highestconcentration of juvenile rearing. Significantstranding periodically occurs in this reach duringhigh flows because many of the floodplainundulations and pits do not drain back to theriver, so as high flows recede, fry and juvenilechinook salmon are stranded and die in theseareas. The remnant dredger tailing surface iscomprised of large cobbles, gravels, and sand,which prohibits natural riparian regeneration.Additionally, substantial loss of the high flowCHAPTER 4167

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 4regime has further discouraged riparian regeneration.Finally, the large volume of sand depositedby the 1997 flood has greatly increased sandstorage in the reach, possibly leading to short-termand long-term negative impacts to chinook salmonhabitat.Project objectivesObjectives for the Basso Spawning Reach FloodplainRestoration Project are:• Increase woody riparian vegetation coverage.• Improve natural regeneration of Fremontcottonwood, valley oak, tree willows and alder.• Remove invasive exotic hardwood vegetation.• Reduce juvenile chinook salmon stranding.• Reduce fine sediment (sand) storage in thefloodway.• Restore functional floodplains.Project descriptionThe project objectives will be achieved byregrading the remnant dredger tailing surfacesinto functional floodplains, and revegetating theserestored floodplain surfaces. Specific componentsinclude:1) Regrade floodway surfaces outside the lowflow channel to inundate at 4,000 to 5,000cfs, thereby increasing bed mobility andrecreating a functional floodplain.Remnant dredger tailing surfaces will beregraded to fill in many of the stranding pits.Other stranding pits and undulations will beregraded so that if flows access them, waterwill drain back to the river and reducechinook salmon stranding. Sand deposited onfloodway surfaces during the 1997 flood willbe preferentially targeted for removal andspoils in pits further away from the channelso the sand will not be re-introduced into theriver for many years. Local areas of highground and old tailings will also be used ason-site fill material to fill pits. We anticipatenear 100,000 yd 3 of earthwork will berequired, with all materials derived on-site.2) Plant native riparian hardwoods on floodwaysurfaces appropriate for each species lifehistory requirements.After earthwork is completed, valley oak,Fremont cottonwood, and willows will beplanted on floodplain surfaces appropriate fortheir life history requirements. Floodplainspecies will be willows, alders and cottonwoods.Willows will be planted nearer theactive channel-bankfull channel transition,while valley oaks will be planted on higherfloodplains and terraces near the vr valleywalls. Revegetation patterns will reflectplant species patterns identified during theriparian inventory conducted in 1996.Because of cost, material supply, and speciescharacteristics, some hardwood species havepriority over others. Cottonwood and willowplantings on floodplain surfaces are prioritizedbecause of their fast growth, structuralcontribution to the riparian corridor, andaesthetics. Valley oaks are the next prioritybecause of their large-scale removal over thepast 100 years. Increasing the valley oakstand size is desirable, not only for theirlong-term wildlife habitat contribution, butalso for the valuable structural componentsthey add to the riparian corridor.Much of the revegetation materials will comefrom on-site sources (valley oak seeds, willowcuttings, cottonwood cuttings), and speciesnot found on-site (sedges, alder, and Oregonash) should be purchased from local nurserieswho obtain it from within the TuolumneRiver corridor. Cluster planting (vegetationpatches) rather than row planting should beencouraged to re-create a more natural siteappearance, ease watering and maintenance,and increase habitat diversity.3) Remove invasive exotic vegetation.All woody exotic plant species within thereach should be removed during floodplainregrading. Three plant species should betargeted for removal: giant reed, tree ofheaven, and all Eucalyptus species. The San168

RESTORING THE TUOLUMNE RIVER CORRIDORJoaquin River Management Program AdvisoryCouncil has identified giant reed as a plant toeliminate throughout the San Joaquin Riverand its tributaries (SJRMP 1995). Eucalyptussp. has been planted and naturalized throughoutthe lower project reach. To ensure that resproutingdoes not occur, the above groundportion and the stump/root wads of exoticplants must be removed. After initial removal,exotic species should be removed in perpetuitybecause these plants prevent nativespecies from naturally recruiting and establishing.4) Preserve existing riparian vegetation.Preserving as much existing native woodyriparian vegetation as feasible is a primarygoal of the project. Cottonwood, tree willow,and valley oak stands should not be removedduring construction. The valley oaks that arepresent in this reach will be utilized for seedcollection, and are important contributors tofuture recruitment. Nearly all cottonwoodsshould be preserved to increase age classdiversity and riparian canopy structure.Mature cottonwoods (>25 years), regardlessof stand size, should not be removed becausethey provide the seed source for futurerecruitment. A few smaller stands (

ADAPTIVE MANAGEMENT5. ADAPTIVE MANAGEMENTThe adaptive management approach outlined asAdaptive Environmental Assessment and Management(AEAM) (Holling 1978) has receivedextensive scientific peer review, and should be thestrategy sought by the Technical AdvisoryCommittee. This approach stresses explicitintegration of scientific, economic and socialconcerns into efforts addressing resource problems.Computer modeling and simulation areemployed to demonstrate the potential effects ofalternative management actions and scientificuncertainty. Stakeholders, all bringing their ownpolitical, economic, and cultural concerns, cometogether in an analytical process aimed atidentifying appropriate cases for scientificinvestigation. Hypotheses and managementobjectives are outlined with prudence anddeliberation (i.e., conservatively).Effective adaptive management must manageprocesses not trends. All too often, monitoring isfashioned with ‘time’ on the X-axis, with thedependent variable (Y-axis) as a responsevariable, often biological. Trend monitoring doesnot target processes that cause the trend, makingcause-and-effect links difficult and qualitative.Additionally, trend monitoring often takes yearsto reveal a consistent trend (e.g., escapement),and usually is a function of several interrelatedfactors.To make and/or refine management recommendations,other variables must be on the X-axis. Inother words, adaptive management must bedriven by hypothesis testing to explain causativeprocesses. This generally means replacing the X-axis with something other than ‘time.’ Forexample, implementing a restoration strategysuch as spawning gravel introduction will requirequantifying the benefits of this activity to the riverecosystem or chinook salmon, such as increasedspawning gravel availability or improvements ingravel permeability, which can then be extendedto quantify the benefit to smolt production orsurvival. Trend monitoring objectives should notbe discarded, but must be integrated with monitoringprotocols that have ‘process’ on the X-axis.CHAPTER 5171

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 5In addition, adaptive management must acknowledgethe uncertainty about the system andresources being managed, favoring actions thatare reversible. Walters and Holling (1990) notethat defining testable hypotheses is trivial, butgenerating hypotheses sensitive to changes in thefunction or processes of the ecosystem is muchmore complex. Restoration actions may shiftlimiting factors from one constraint to another,confounding the interpretation of experimentalresults, even though improvements were realized.They suggest a blend of “scale-constrainedmodels, scale-unconstrained process knowledge,good old-fashioned natural history and activeadaptive management.”The first and primary objective of an adaptivemanagement plan is to define policy and managementobjectives. We believe that the Attributes ofRiver Ecosystem Integrity (presented in Chapter2) provide a foundation for management objectives.as an integral component.The second objective is to document the statusand trends in chinook salmon population dynamics,continuing with the outlined FERC-mandatedmonitoring plan. These biological objectivesshould include all in-river salmon life stages, behabitat based, and should target preventing largepopulation crashed such as occurred in responseto drought years.The third objective, intertwined with the first twoobjectives, is to define restoration endpoints:• What is/will be meant by “self-sustaining”ecosystem processes? Can we achieve this, orwill human intervention be necessaryindefinitely?• How much can we expect anadromous salmonidhabitat or population levels to respond (andimprove) to restoration activities?• Can we restore the processes that sustainnatural regeneration of riparian vegetation?These questions will be critically important as theRestoration Plan is implemented.Successful adaptive management requires aprocess for identifying and evaluating sciencebasedhypotheses, and then formulating strategiesto meet management objectives. Adaptivemanagement also requires a sound monitoringplan to provide the scientific basis for changingmanagement strategies. In other words, a strongfeedback loop that includes formulation ofhypotheses, implementation, monitoring, managementevaluation, and finally, managementresponse, is fundamental. Because restorationactivities will be substantial in the coming years,two roles of monitoring are needed: river-wideand restoration project-specific. We emphasizethat the recommendations and framework foradaptive management provided by this monitoringplan provide only the scientific basis forimplementing monitoring, while the task ofdefining policy and management objectives(Objective 1) is left to the Technical AdvisoryCommittee.5.1. MONITORINGThe purpose of the Tuolumne River MonitoringProgram is to provide a quantitative basis forevaluating the success of management actionsimplemented under the FERC Settlement Agreementadaptive management strategy, and fordetermining whether the “comparative goals” setforth in the Settlement Agreement are met (TID1998).While an extensive foundation of informationalready exists for the Tuolumne River, perhapsmore complete than most other Central Valleyrivers, there is nevertheless a need for moreinformation to assess the success of futurerestoration and management actions. Carefulplanning and documentation are essential.Despite substantial information generated overthe past years on the Tuolumne River, geomorphicand physical-process data have received lessattention. Past monitoring, along with FSAprescribedmonitoring focus on chinook salmonproduction, survival, and population levels. Nomonitoring program has been developed to assessphysical processes that maintain river conditionsand integrate chinook salmon objectives andrestoration activities. We propose objectives andsuggest a framework for a river-wide monitoringprogram that incorporates objectives of the FSA,the Draft Monitoring Program developed by theDistricts, and project-specific monitoring associatedwith restoration projects such as the SRP 9/10 and Gravel Mining Reach projects.In addition to river-wide monitoring objectives,Section 12 of the FSA requires a program thatintegrates with site-specific monitoring designedto evaluate specific project objectives. The172

ADAPTIVE MANAGEMENTmonitoring program should be approved by theTRTAC (i.e., TRTAC should evaluate andapprove or modify the information presentedhere). Section 13 requires the Districts, incooperation with CDFG, USFWS, and CCSF, tomonitor the fall-run chinook salmon and theirhabitat. Many components of Section 13 monitoringhave been implemented or are scheduled to beimplemented in the near future. In addition toriver-wide monitoring required by the FSA,agencies issuing permits or providing funds toimplement restoration program componentsrequire site-specific monitoring to assure thatproject objectives and desired benefits areachieved, and negative impacts are avoided ormitigated. Monitoring identified in the FSASections 12 and 13 consists of these two integratedcomponents: a river-wide component and arestoration site-specific component. These twocomponents are summarized as:The river-wide component should assess largescaleprocesses, characteristics, and trends,providing information necessary to evaluate theoverall effectiveness of flow and non-flowmanagement measures. The monitoring specifiedin FSA Section 13 focuses on assessing salmonpopulation dynamics, habitat utilization, and thesuccess of the restoration program in restoring thepopulation to acceptable levels and increasing thepopulation’s resiliency on a river-wide basis. Inaddition to habitat and salmon populationparameters to be monitored under FSA Section13, the river-wide component may includeassessment of fluvial and ecological processes andresponses of river, floodplain, and riparianecosystems to those processes as a result of FSASection 12 restoration efforts. For example,monitoring may document that the restorationprogram increased spawning and rearing habitatquantity and quality, reduced habitat for introducedpredatory fish, and increased riparianvegetation cover. The Section 13 monitoringprogram would assess whether this improvementin physical habitat resulted in improved salmonproduction or recruitment.The restoration site-specific component shouldevaluate and measure the success of specificrestoration projects. The river-wide componentassesses fluvial geomorphic and ecologicalprocesses and response to restoration measures atthe scale of the entire river corridor or reach,while the site-specific component assesses similarquestions within or near the spatial boundaries ofa specific restoration project. For example, sitespecificmonitoring for a channel restorationproject might assess sediment transport throughthe reconstructed channel, the performance of thedesigned bankfull channel, changes in eggemergence success, and germination of nativeriparian vegetation within the site. Site-specificmonitoring will be as important on the TuolumneRiver as river-wide strategies to evaluate theefficacy of restoration actions, and then refine,recommend, or re-prioritize activities in otherdirections. Sites-specific monitoring could also befunded by outside funding sources, addressingissues that compliment FERC monitoring but arenot currently funded by the FSA. This sitespecificinformation can be used for a river-wideassessment.Below we present river-wide monitoring protocolsto illustrate the broad range of information needs,and to aid in prioritizing monitoring objectives.These protocols incorporate those mandated bythe FSA, and also incorporates monitoring thatintegrates physical processes with riparian andfisheries resources. This monitoring plan is notintended to be exhaustive, acknowledging thatmany finer-scale ecological processes are beyondthe scope of this Plan.5.2. RIVER-WIDE MONITORINGPROTOCOLS FOREVALUATING FLUVIALPROCESSES AND SALMONIDPOPULATION RECOVERYSEDIMENT BUDGET AND ROUTING• Document thresholds for channelbed mobility,related to flood frequency;• Document changes in instream gravel storageto ensure salmonid spawning and rearinghabitats are not limited by gravel availability;• Document fine and coarse bedload transportrates as a function of discharge magnitude,duration, and frequency in the gravel-beddedreaches, combining field sampling andmodeling;• Document occurrence and future formation oflarge-scale alluvial features, e.g., point bars;CHAPTER 5173

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 5CHANNELBED DYNAMICS ANDMORPHOLOGY• Document changes in channel morphology(e.g., riffle loss, channel downcutting oraggradation, channel migration, cross sectionaladjustments, channelbed surface composition);• Document the extent (scour depth) and frequencyof channel-bed surface mobility,spawning gravel deposits, and larger alluvialfeatures (e.g., point bars) as a function ofannual high flow magnitude, duration andfrequency;FLOODPLAIN AND RIPARIAN DYNAMICS• Document increases in areal extent of functionalfloodplain (suitable for dynamic cottonwooddevelopment);• Record status of encroached alders alongchannel margins of selected index reaches.(considerable mortality occurred prior to theJanuary 1997 flood presumably from prolongedinundation by higher baseflows);• Document volume and areal extent of finesediment deposition on floodplain surfacesrelated to flood frequency;• Document species diversity, age class composition,and physical microclimate of ripariancommunities on selected floodplains and lowterraces, including temperature reduction andincreased humidity within the riparian canopy.Large stands of trees that can modify microclimatehave conspicuously higher relativehumidity inside the stand than outside, and canbetter sustain riparian-dependent plant andanimal communities.SALMON SPAWNING AND REARINGHABITAT• Document river-wide spatial and temporalchanges in spawning gravel quality (via particlesize analysis and/or permeability or othersimilar methods) resulting from larger andmore frequent high flow releases and reducedfine sediment supply;• Document river-wide spatial and temporalchanges in spawning habitat quantity (using asystematic habitat classification system andhigh resolution aerial photographs in field)resulting from larger and more frequent highflow releases and greater gravel supply;• Document occurrence and quality of juvenilechinook rearing habitat in relation to selectedsites with alluvial features, rip-rapped banks,etc. by mapping potential habitat for targetspecies. A subset of these sites could serve ascontrol sites for evaluating success of specificchannel reconstruction projects;• Evaluate the heterogeneity (complexity) ofhabitat in relation to variable flows at themicrohabitat and macrohabitat levels;• Integrate fluvial geomorphic restorationobjectives (e.g., gravel management program)with chinook habitat (e.g., spawning habitat) byquantifying habitat availability in relation togeomorphic features (e.g., alternate bars);SALMON POPULATION DYNAMICS• Estimate survival (reach and river-wide) andproduction, physiological condition, origin(wild or hatchery), and timing of downstreammigrating smolt populations;• Estimate adult escapement with annual spawningsurveys, or an adult counting station;• Document spatial and temporal trends in reddconstruction, superimposition, and abundance;• Evaluate genetic composition of TuolumneRiver salmon stocks;• Document salmonid straying from nearby rivers(from carcass surveys);• Perform scale analyses to estimate smolt sizethat produces the highest proportion of adultspawners;• Refine and implement the salmonid populationmodel and/or other strategies to continuallyevaluate limiting factors;OTHER FISH POPULATIONS• Document annual population trends forSacramento squawfish, largemouth bass,smallmouth bass, and others, using indexreaches distributed throughout the lowerTuolumne River;• Document spawning habitat location, extent,and seasonal utilization of largemouth bass andsmallmouth bass;• Document relationship between water temperatureand largemouth bass recruitment;174

ADAPTIVE MANAGEMENTWILDLIFE POPULATIONS• Document location, seasonal utilization, sitecharacteristics, and population size in heronand egret rookeries, osprey nest sites, (andother wildlife species, especially listed species)within the riparian corridor;• Record influence of riparian corridor width onwildlife species diversity (presently, no one canrecommend a minimum riparian corridor widthappropriate to the Tuolumne River corridor thatrestores and maintains riparian plant andanimal communities because no monitoringdata have been collected that target thisconcern);• Inventory occurrence and utilization of largesnags in the riparian corridor;• Survey index reaches for inventorying amphibianspecies diversity and populations;• Survey index reaches for inventoryingmacroinvertebrate species diversity andpopulations;WATER QUALITY• Continuously record ambient water temperaturesfrom La Grange Dam to the San JoaquinRiver confluence;• Continuously record ambient water temperaturein potential thermal refugia during summer andearly fall;• Evaluate variations in water temperature at themicrohabitat level (e.g., determine if watertemperatures in pools are stratifying, and ifthermal stratification is a function of riverdischarge);• Document seasonal patterns of dissolvedoxygen concentration and turbidity throughoutthe lower Tuolumne River and at suspectedpoint sources;• Develop a program to evaluate sources andimpacts of pesticide, herbicide and hydrocarbonrunoff on the aquatic community in themainstem Tuolumne River;• Monitor discharge from Dry Creek to assesswater quality effects on Tuolumne Rivermainstem;INTEGRATION• Integrate disparate information needs intocohesive monitoring plan.Obviously a comprehensive monitoring plan mustbe more than simply lists of data collectionprotocols or sampling strategies. With no cohesivestrategy, data collection will follow managementactions instead of lead them, as an adaptivemanagement plan would require. Integrating orsynthesizing information needs into a wellorganized strategy to collect, interpret, then reviseobjectives is the single most important step indeveloping a monitoring plan.As an initial step, conceptual models should bedeveloped that integrate existing experience andscientific information and are capable of makingpredictions about the river system, and about theimpacts of alternative policies or actions. Thesemodels can then identify key knowledge gaps thatmake model predictions questionable. These gapsshould be a primary target of monitoring, with theintention of fortifying the model, and thereforeour understanding of how the river works.As an example, the Districts developed a stockrecruitmentmodel (EA 1992, 1997) for the SanJoaquin River chinook salmon population toexplain the dynamic fluctuations in populationlevels, and to explore the role of environmental(mortality) factors in explaining these fluctuations.Once calibrated, the model can predictchinook salmon population changes to “adaptivemanagement or restoration activities” such asspring pulse flows, increased availability of highquality spawning habitat, decreased bass predation,or improvements in water quality. Thesepredictions can then help prioritize managementstrategies. The predictions are then tested bymonitoring and field experimentation. Thesalmon population model, like all models, hasweaknesses. Adult escapement estimates for theSan Joaquin River basin tributaries could bereplaced by actual escapement counts by constructinga fish weir or other trapping/countingprocedure, to eliminate uncertainty in the estimationof these model parameters. These counts canthen be used to calibrate carcass survey estimates.Other weaknesses of the model include theaccurate aging of returning adults, and anaccurate means of evaluating juvenile production,both of which would increase the utility of thismodel as a management tool.CHAPTER 5175

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCHAPTER 5In addition to chinook salmon models, processbasedmodels are essential in making managementdecisions. Process-based models can oftenbe calibrated more precisely than biologicalmodels. For example, a central feature of theRestoration Plan is restoring coarse sedimentsupply and bedload transport processes in theupper Tuolumne River spawning reaches, withthe explicit goal of improving spawning habitat.Balancing coarse sediment supply with higherdischarges capable of mobilizing and transportingcoarse sediment is an essential feature of thisrestoration strategy, and should be accomplishedby a combination of field measurements andmodeling. Spawning gravel management toimprove habitat availability and egg survival-toemergencecan be field tested (e.g., with permeabilitymethods currently being developed). Theimportant point is that policy or managementdecisions must be made as explicit, testablehypotheses that are then evaluated to determinetheir efficacy. Models can provide the foundationfor determining which hypotheses (managementactions) have the best chance of succeeding andforecasting their effects on salmon production.5.3. CHINOOK SALMONMONITORING UNDER THEFERC SETTLEMENTAGREEMENTThe Districts have developed a monitoring plan(TID 1998) designed to meet chinook salmonmonitoring requirements of the FERC SettlementAgreement. This plan is incorporated here as afoundation for continued monitoring of thechinook salmon population and habitat in theTuolumne River.5.3.1. River-wide monitoring (FSASection 13)The chinook salmon monitoring plan (Section 13)focuses on salmon biology, water temperature,and spawning habitat quality. Information onother fish species is also gathered in this monitoring.The Districts have also developed a proposal(TID 1997) to integrate monitoring of fry,juvenile, and smolt life stages. The proposalincludes three main components: (1) monitoringchinook salmon size, distribution, abundance,migration, production, and survival; (2) assessingrearing conditions in the San Joaquin River,and (3) completing the flow fluctuation andstranding assessment for fry and juvenile salmon.The fry, juvenile, and smolt monitoring proposal(TID 1997) incorporates the ComprehensiveAssessment and Monitoring Program (CAMP)directed by the US Fish and Wildlife Service,which will document fry, juvenile, and smoltproduction from the Tuolumne River as well asemigration timing and the effects of variousfactors on emigration timing. The CAMPassessment will be based on data collected at arotary screw trap installed near the mouth of theTuolumne River. The trap will be monitored fromJanuary 1 through June 30 each year. A detaileddescription of the trap monitoring protocol is inStandard Protocol for Rotary Screw Trap Samplingof Outmigrating Juvenile Salmonids(USFWS 1997).Monitoring chinook salmon migration, production,and survival would be based on the operationof two rotary screw traps, one near thedownstream end of the spawning reaches (andcorresponding with the upstream end of theGravel Mining Reach), and one at the downstreamend of the Gravel-bedded Zone. Samplingprocedures would follow CAMP protocols(USFWS 1997). The following hypotheses wouldbe tested:• Fry, juveniles, and smolts emigrating from theTuolumne River experience significant mortalitybefore reaching the San Joaquin River.• Fry, juveniles, and smolts rearing and emigratingfrom the Tuolumne River may experiencehigher mortality in the mined reach (from nearTurlock Lake State Recreation Area (TLSRA)to Hughson Sewage Treatment Plant) than inthe downstream reach (from Hughson SewageTreatment Plant to Shiloh Road) or the spawningreach upstream of TLSRA.• Migration timing and rate are influenced byenvironmental factors, including flow magnitude,flow changes, turbidity, and/or watertemperature.• Migration timing is influenced by smolt size.• Fry and juvenile salmon are unequally distributedin the lower river.• Distribution of rearing juveniles is influencedby environmental factors, including flowmagnitude, turbidity, and/or water temperature.176

ADAPTIVE MANAGEMENT• Distribution of rearing juveniles is influencedby fish size.5.3.2. Site-specific monitoring objectivesSite-specific monitoring (related to implementationof restoration projects) offers the opportunityto address river-wide objectives at a site-specificscale. Information gathered to assess projectobjectives can be designed to address broaderobjectives and knowledge gaps. While sitespecificmonitoring objectives should targetrestoration project objectives, they should includea river-wide perspective. For example, smoltsurvival studies designed to evaluate the SRP 9/10Channel Restoration Projects were integrated intothe river-wide monitoring to achieve multipleobjectives and share monitoring costs. Thisapproach is encouraged wherever practicable.In general, site-specific monitoring will assesswhether: (1) the intended physical features wereconstructed as designed, (2) the hydraulic andfluvial processes function as intended, (3) targetedbiological taxa and communities (especiallysalmon) receive intended benefits, and (4) thesebiological and physical components, oncerestored, will be self-sustaining in the futurehydrologic regime.5.3.3. Summary of completed, ongoing,and proposed monitoring efforts(in addition to FSA section 13)The TID/MID, CDFG, and USFWS conductedextensive monitoring on the Tuolumne Riverprior to the 1995 FSA as part the Don PedroProject FERC Fish Study Programs and otherinvestigations. In addition, analyses of fluvialgeomorphic and ecological processes are includedin this Restoration Plan.Three monitoring components are describedbelow. The smolt survival monitoring programcurrently being implemented on the TuolumneRiver includes two independent, integratedstrategies: (1) large coded-wire tagged juvenileand smolt releases to assess the relationshipbetween survival during outmigration, andconcurrent streamflows, and (2) a multiplemarkedrecapture strategy designed to providereach-specific outmigration survival and timingdata. Implementation of this strategy is tentativelyscheduled to continue during the next two years,but is currently under close review by the TechnicalAdvisory Committee.The assessment of rearing conditions in the SanJoaquin River would include a two-year reconnaissance-levelsurvey to: (1) develop a suitablebase map of habitat, (2) review literature, (3)evaluate temperature and water quality data, (4)assess prey species and food supply, (5) surveypredator species more comprehensively than hasbeen done in the past (6), and assess chinooksalmon abundance and distribution (based onUSFWS and District seining surveys. Thisreconnaissance would be used to develop hypothesesfor future studies. The San Joaquin Rivermonitoring should be a TRTAC or joint agencyresponsibility because of restoration efforts onother rivers.The juvenile stranding/flow fluctuation study(proposal accepted by the TRTAC December1997) would build on stranding and entrapmentstudies previously conducted by the Districts.Juvenile stranding has been documented by fieldsurveys since 1987. These surveys focused onareas known, or suspected, to pose a high strandingrisk. However, they did not completely assessstranding risk. The proposed program would: (1)catalogue sites surveyed in previous studies, (2)identify potential stranding sites from the existingGIS database, (3) identify slope, substrate, andentrapment area at various sites, (4) conductsurveys to document stranding and entrapment ata sample set of sites under various flow conditions(estimated 10 surveys, 2.5 days each over 2years), (5) identify sites where highest strandingrates are likely to occur based on site conditionsand observations, and (6) determine relativesignificance of stranding losses. These assessmentswill be used to: (a) develop a prioritized listof stranding sites to be addressed by channel orfloodplain restoration or other methods, and (b)identify flow operations or other managementactions to reduce stranding risks. These monitoringefforts are described by Ford (TID 1998) andsummarized in the “Draft Proposal for LowerTuolumne River Salmon Fry, Juvenile, and SmoltDistribution and Survival Monitoring” (TID1997) distributed to the TRTAC in December1997. Detailed descriptions of the studies andtheir findings can be found in reports submitted toFERC by the TID/MID.CHAPTER 5177

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR5.3.4. SummaryAdaptive management is essential to successfulimplementation of the Restoration Plan. Adaptivemanagement will not only improve managementpolicy and restoration actions, but also will extendour knowledge of the river ecosystems. These areambitious goals for any program, but much moreso for a program attempting large-scale ecologicalrestoration of a river the size of the TuolumneRiver. Add the socioeconomic uncertainties, andthe task of restoring the river becomes daunting.But this acknowledgement does not justifyinaction, and the stakeholders involved in theimplementation of this Restoration Plan must bewilling to accept slow progress, investment ofsubstantial amounts of time and money, and therisks involved in decision making. We mustacknowledge the inherent uncertainty of ouractions, weigh possible outcomes with considerablecaution, then proceed with the best scienceavailable.CHAPTER 5178

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REFERENCESTID (Turlock Irrigation District). Tiered Environmental Assessment and Initial Study/Mitigated NegativeDeclaration. US Fish and Wildlife Service-Anadromous Fish Restoration Program, Tuolumne RiverRiparian Zone Improvements. Gravel Mining Reach & Special Run Pools 9/10 Restoration and Mitigationprojects. Turlock Irrigation District, Turlock, CA. US Fish and Wildlife Service, Sacramento Field Office,Sacramento, CA.Tietje, W., R. Barrett, Kleinfelter, E. and B. Carre. Wildlife diversity in oak riparian habitat: northcentral vs. central coast California. Symposium on oak woodlands and hardwood rangeland management,Pacific Southwest Research Station, Berkeley, CA, U. S. Forest Service.Trinity Restoration Associates. Historical channel analysis Tuolumne River mile 37.4-39.6. Prepared forM.J.Ruddy & Son, Sonora, CA.USFWS. The needs of chinook salmon (Oncorhynchus tshawytscha) on the Sacramento- San Joaquinestuary. California Water Resources Control Board. Sacramento, CA.USFWS. Measures to improve the protection San Joaquin fall-run chinook salmon in the Sacramento/San Joaquin River delta. California Water Resources Control Board. Sacramento, CA.USFWS. Comprehensive Assessment and Monitoring Program (CAMP) Implementation Plan: Acomprehensive Plan to Evaluate the Effectiveness of CVPIA Actions in Restoring Anadromous FishProduction. Sacramento CA.USFWS (US Fish and Wildlife Service). Trinity River Flow Evaluation Final Report. Report to theSecretary, US Department of the Interior, Washington, D.C.USGS (US Geological Survey). Determination of channel capacity of the Tuolumne River downstreamfrom La Grange, Stanislauas County, California. , USGS Watern Resources Division, Menlo Park, CA.USGS (US Geological Survey). Guidelines for determining flood flow frequency. Reston, VA. Office ofWater Data Collection. 27 pp.Verner, J., and A.S. Boss (eds.). California wildlife and their habitats: western Sierra Nevada. US ForestService. Berkeley CA. General Technical Report PSW-37.Walters, C.J., and C.S. Holling. “Large-scale management experiment and learning by doing”. Ecology71(6):2060-2068.Warner, R. E. and K. M. Hendrix (eds.). California riparian systems: ecology, conservation, andproductive management. Berkeley, CA. University of California Press.Wilcock, P. A method for predicting sediment transport in gravel-bed rivers. Johns Hopkins University,Baltimore.Wolman, M. G. “A method of sampling coarse river-bed material.” Transactions of the AmericanGeophysical Union 35: 951-956.Yoshiyama, R.M., F.W. Fisher, and P.B. Moyle. Historical abundance and decline of chinook salmon inthe Central Valley region of California. North American Journal of Fisheries Management 18: 487-521.APPENDICESAppendix A. Tuolumne River at La Grange annual hydrographsAppendix B. Tuolumne River series lists, species lists, and riparian inventory mapREFERENCES183



TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORAPPENDIX A30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001918, unregulated NORMAL Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001919, unregulated DRY Water Year1-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001920, unregulated DRY Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001921, unregulated NORMAL Water Year1-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep186

APPENDIX A30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepAPPENDIX A1922, unregulated WET Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001923, unregulated NORMAL Water YearDaily Average Discharge (cfs)30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep1924, unregulated CRIT DRY Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001925, unregulated NORMAL Water YearDaily Average Discharge (cfs)187

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORAPPENDIX A30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001926, unregulated DRY Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001927, unregulated WET Water Year1-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001928, unregulated NORMALWater Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001929, unregulated CRIT DRY Water Year1-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep188

APPENDIX A30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepAPPENDIX A1930, unregulated DRY Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001931, unregulated CRIT DRY Water YearDaily Average Discharge (cfs)30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001932, unregulated WET Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001933, unregulated DRY Water Year1-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep189

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORAPPENDIX A30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001934, unregulated CRIT DRY Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001935, unregulated WET Water Year1-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001936, unregulated WET Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001937, unregulated NORMAL Water Year1-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep190

APPENDIX A30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001-Oct1-Nov1-DecDaily Average Discharge (cfs)1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep74,421 cfsAPPENDIX A1938, unregulated EX WETWater Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001939, unregulated CRIT DRY Water YearDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001940, unregulated WETWater Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001941, unregulated WET Water Year1-Oct1-Nov1-DecDaily Average Discharge (cfs)1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep191

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORAPPENDIX A30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001942, unregulated WET Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001943, unregulated WET Water Year1-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001944, unregulated DRY Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep45,420 cfs1945, unregulated WETWater YearDaily Average Discharge (cfs)192

APPENDIX A30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepAPPENDIX A1946, unregulated NORMAL Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001947, unregulated CRIT DRY Water YearDaily Average Discharge (cfs)30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001948, unregulated NORMAL Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001949, unregulated DRY Water Year1-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep193

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORAPPENDIX A30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001950, unregulated NORMAL Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001951, unregulated WET Water Year43,557 cfs1-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001952, unregulated EX WET Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,000066,959 cfs1953, unregulated NORMAL Water Year1-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep194

APPENDIX A30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001-Oct1-Nov1-DecDaily Average Discharge (cfs)1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepAPPENDIX A1954, unregulated NORMAL Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001955, unregulated DRY Water YearDaily Average Discharge (cfs)30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001956, unregulated EX WET Water Year1-Oct1-Nov1-DecDaily Average Discharge (cfs)1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep118,338 cfs30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001957, unregulated NORMAL Water YearDaily Average Discharge (cfs)195

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORAPPENDIX A30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001958, unregulated EX WET Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001959, unregulated CRIT DRY Water Year1-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001960, unregulated CRIT DRY Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001961, unregulated CRIT DRY Water Year1-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep196

APPENDIX A30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepAPPENDIX A1962, unregulated NORMAL Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001963, unregulated NORMAL WaterYearDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001964, unregulated DRY Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,000070,014 cfs1-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep72.693 cfs1965, unregulated EX WET Water YearDaily Average Discharge (cfs)197

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORAPPENDIX A30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001966, unregulated DRY Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001967, unregulated EX WET Water Year1-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001968, unregulated CRIT DRY Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001969, unregulated EX WETWater Year1-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep198

APPENDIX A30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepAPPENDIX A1970, regulated1970, unregulated EX WETWater Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001971, regulated1971, unregulated NORMAL Water YearDaily Average Discharge (cfs)30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001972, regulated1972, unregulated DRY Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001973, regulated1973, unregulated WET Water Year1-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep199

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORAPPENDIX A30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001974, regulated1974, unregulated WET Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001975, regulated1975, unregulated WET Water Year1-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001976, regulated1976, unregulated CRIT DRY Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001977, regulated1977, unregulated CRIT DRY Water Year1-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep200

APPENDIX A30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001-Oct1-Nov1-Dec1-JanDaily Average Discharge (cfs)1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepAPPENDIX A1978, regulated1978, unregulated EX WET Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001979, regulated1979, unregulated NORMAL Water YearDaily Average Discharge (cfs)30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001980, regulated1980, unregulated EX WETWater Year1-Oct1-Nov1-Dec1-JanDaily Average Discharge (cfs)1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep58,383 cfs30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001981, regulated1981, unregulated DRY Water YearDaily Average Discharge (cfs)201

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORAPPENDIX A30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001982, regulated1982, unregulated EXWET Water Year1-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep49,259 cfs52,118 cfs30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001983, regulated1983, unregulated EX WET WaterYearDaily Average Discharge (cfs)30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001984, regulated1984, unregulated WET Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001985, regulated1985, unregulated DRY Water Year1-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep202

APPENDIX A30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepAPPENDIX A53,179 cfs1986, regulated1986, unregulated EX WETWater Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001987, regulated1987, unregulated CRIT DRY Water YearDaily Average Discharge (cfs)30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001988, regulated1988, unregulated CRIT DRY Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001989, regulated1989, unregulated DRY Water Year1-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep203

TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORAPPENDIX A30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001990, regulated1990, unregulated CRIT DRY Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001991, regulated1991, unregulated DRY Water Year1-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001992, regulated1992, unregulated CRIT DRY Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001993, regulated1993, unregulated EX WET Water Year1-Oct1-NovDaily Average Discharge (cfs)1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep204

APPENDIX A30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001994, regulated1994, unregulated DRY Water Year1-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Jan1-Nov1-Dec1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepAPPENDIX A30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,000046,631 cfs1995, regulated1995, unregulated EX WETWater YearDaily Average Discharge (cfs)30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001996, regulated38,425 cfs1996, unregulated WET Water Year30,00028,00026,00024,00022,00020,00018,00016,00014,00012,00010,0008,0006,0004,0002,00001-Oct1-Nov1-Dec1-Jan1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-SepDaily Average Discharge (cfs)1-Oct1-Jan1-Nov1-Dec1-Feb1-Mar1-Apr1-May1-Jun1-Jul1-Aug1-Sep130,000 cfs50,100 cfs1997, unregulated1997, regulatedDaily Average Discharge (cfs)205



APPENDIX B208VEGETATION SERIESNATURAL DIVERSITY DATA BASE/HOLLAND TYPETHE NATURECONSERVANCY "ASSOCIATED" SPECIESHABITAT OBSERVEDSTATUS INDEX1) Arroyo willow series Southern cottonwood-willow riparian forest (61330 in part ) G3 S3 Salix lasiolepisGreat Valley cottonwood riparian forest (61410 in part ) G3 S2.1 Cephalanthus occidentalisGreat Valley mixed riparian forest (61420 in part ) G2 S2.1 Populus fremontiiSouthern willow scrub (63320 in part ) G3 S3.2 Rubus discolorSambucus mexicana2) Black willow series Southern cottonwood-willow riparian forest (61330 in part ) G3 S3 Salix gooddingiiGreat Valley cottonwood riparian forest (61410 in part ) G3 S2.1 Alnus rhombifoliaGreat Valley mixed riparian forest (61420 in part ) G2 S2.1 Ailanthus altissimaSouthern willow scrub (63320 in part ) G3 S3.2 Arundo donaxCephalanthus occidentalisFraxinus latifoliaPopulus fremontiiQuercus lobataRubus discolorSalix exiguaSalix lasiolepisSalix laevigataSalix lucida ssp. lasiandraSalix melanopsis3) Blue elderberry series Elderberry savanna (63430) G2 S2.1 Sambucus mexicanaMexican elderberry seriesAilanthus altissimaFraxinus latifoliaPopulus fremontiiQuercus lobataRubus discolorSalix exiguaVitis californica4) Blue oak series Blue oak woodland (71140) G3 S3.2 Quercus douglasiiDigger pine-oak woodland (71410 in part ) G4 S4 Ailanthus altissimaPinus sabianaQuercus lobataQuercus wislizeniiTUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR

VEGETATION SERIESNATURAL DIVERSITY DATA BASE/HOLLAND TYPETHE NATURECONSERVANCY "ASSOCIATED" SPECIESHABITAT OBSERVEDSTATUS INDEX2095) Box elder series Proposed series N/A Acer negundo var. californicumSalix exiguaSalix lasiolepis6) Buttonbush series Buttonbush scrub (63430) G1 S1.1 Cephalanthus occidentalisAlnus rhombifoliaSalix exiguaSalix lucida ssp. lasiandragraminoids7) California buckeye series Mixed north slope forest (81500) G4 S4 Aesculus californicaFicus caricaFraxinus dipetala7) California buckeye series, con’t Pinus sabianaQuercus lobataQuercus douglasiiQuercus wislizenii8) California walnut series California walnut woodland (71210) G2 S2.1 Juglans californicaWalnut forest (81600) G1 S1.1 Fraxinus dipetalaSambucus mexicana9) Dusky willow series Proposed series N/A Salix melanopsisSalix exiguaSalix lasiolepisSalix lucida ssp. lasiandra10) Eucalyptus series EXOTIC N/A Eucalyptus camaldulensisEucalyptus globulusEucalyptus polyanthemosEucalyptus tereticornis11) Edible fig series EXOTIC Proposed series N/A Ficus caricaRubus discolorVitis californicaAPPENDIX BAPPENDIX B

APPENDIX B210VEGETATION SERIESNATURAL DIVERSITY DATA BASE/HOLLAND TYPETHE NATURECONSERVANCY "ASSOCIATED" SPECIESHABITAT OBSERVEDSTATUS INDEX12) Fremont cottonwood series Great Valley cottonwood riparian forest (61410 in part ) G3 S2.1 Populus fremontiiGreat Valley mixed riparian forest (61420 in part ) G2 S2.1 Acer negundo var. californicumAilanthus altissimaArundo donaxFicus caricaFraxinus latifoliaJuglans californicaMorus albaQuercus lobataRubus discolorSalix exiguaSalix gooddingiiSalix lasiolepisSalix laevigataSalix lucida ssp. lasiandraSalix melanopsisToxicodendron diversilobumVitis californica13) Giant reed series EXOTIC N/A Arundo donaxSalix exigua14) Interior live oak series Interior live oak woodland (71150) G3 S3.2 Quercus wislizeniiInterior live oak forest (81330) G4 S4 Pinus sabianaQuercus douglasii15) Lamb’s quarter’s series EXOTIC Proposed series Chenopodium albumTUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR

VEGETATION SERIESNATURAL DIVERSITY DATA BASE/HOLLAND TYPETHE NATURECONSERVANCY "ASSOCIATED" SPECIESHABITAT OBSERVEDSTATUS INDEX21116) Mixed willow series Freshwater swamp (52600 in part ) G1 S1.1 Acer negundo var. californicumGreat Valley cottonwood riparian forest (61410 in part ) G3 S3 Alnus rhombifoliaGreat Valley mixed riparian forest (61420 in part ) G3 S2.1 Arundo donaxGreat Valley willow scrub (63410 in part ) G2 S2.1 Ficus caricaSouthern willow scrub (63320 in part) G3 S3.2 Fraxinus latifoliaPopulus fremontiiQuercus lobataRubus discolorSalix babylonicaSalix exiguaSalix gooddingiiSalix lasiolepisSalix laevigataSalix lucida ssp. lasiandraSalix melanopsisVitis californica17) Narrow-leaf willow series Southern cottonwood-willow riparian forest (61330 in part ) G3 S3 Salix exiguaGreat Valley cottonwood riparian forest (61410 in part ) G3 S2.1 Alnus rhombifoliaGreat Valley willow scrub (63410 in part ) G3 S3.2 Arundo donaxCephalanthus occidentalisPopulus fremontiiQuercus lobataSalix gooddingiiSalix lasiolepisSalix laevigataSalix lucida ssp. lasiandraSalix melanopsis18) Oregon ash series Proposed series N/A Fraxinus latifoliaAlnus rhombifoliaSalix exiguaAPPENDIX BAPPENDIX B

APPENDIX B212VEGETATION SERIESNATURAL DIVERSITY DATA BASE/HOLLAND TYPETHE NATURECONSERVANCY "ASSOCIATED" SPECIESHABITAT OBSERVEDSTATUS INDEX19) Shining willow series Freshwater swamp (52600 in part ) G1 S1.1 Salix lucida ssp. lasiandraSouthern cottonwood-willow riparian forest (61330 in part ) G3 S3 Alnus rhombifoliaGreat Valley mixed riparian forest (61420 in part) G3 S2.1 Fraxinus latifoliaGreat Valley cottonwood riparian forest (61410 in part ) G2 S2.1 Populus fremontiiGreat Valley willow scrub (63410 in part ) G3 S3.2 Quercus lobataPacfic willow seriesRubus discolorSalix exiguaSalix gooddingiiSalix laevigataSalix lasiolepisSalix melanopsisVitis californica20) Tree of heaven series EXOTIC Proposed series N/A Ailanthus altissima21) Valley oak series Great Valley valley oak riparian forest (61430) G1 S1.1 Quercus lobataValley oak woodland (71130) G2 S2.1 Aesculus californicaAilanthus altissimaMorus albaPopulus fremontiiQuercus douglasiiQuercus wislizeniiRubus discolorSalix melanopsisToxicodendron diversilobumVitis californica22) White alder series White alder riparian forest (61510) G3 S3 Alnus rhombifoliaCephalanthus occidentalisFraxinus latifoliaRubus discolorSalix exiguaTUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR

Nature Conservancy Heritage Program Status RanksGlobal ranksG1= Fewer than 6 viable occurrences worldwide and/or 2000 acresG2= 6-20 viable occurrences worldwide and/or 2,000-10,000 acresG3= 21-100 viable occurrences worldwide and/or 10,000-50,000 acresG4= Greater than 100 viable occurrences worldwide and/or greater than 50,000 acresG5= vegetation type is demonstrably secure due to worldwide abundanceState ranksS1= Fewer than 6 viable occurrences statewide and/or 2000 acresS2= 6-20 viable occurrences statewide and/or 2,000-10,000 acresS3= 21-100 viable occurrences statewide and/or 10,000-50,000 acresS4= Greater than 100 viable occurrences statewide and/or greater than 50,000 acresS5= vegetation type is demonstrably secure statewideThreat Ranks0.1 = Very threatened0.2 = Threatened0.3 = No current threats knownReferences:Hickman J.C. (Ed.) 1993. The Jepson Manual Higher Plants of California .University of California Press, Berkeley.213Sawyer J.O. and Keeler-Wolf T. 1995. A Manual of California Vegetation .California Native Plant Society.APPENDIX BAPPENDIX B

APPENDIX B214Scientific Name Common Name Locality Habit USFWS Hydric Code SCS Code1 Acer negundo var. californicum Box Elder N Tree FACW ACNEC22 Aesculus californica California Buckeye N Tree AECA3 Ailanthus altissma Tree of Heaven IE Tree FACU AIAL4 Alnus rhombifolia White Alder N Tree FACW ALRH25 Eucalyptus camaldulensis Red Gum, River Red Gum IE Tree EUCA26 Eucalyptus sp. Gum Tree IE Tree EUSP*7 Fraxinus latifolia Oregon Ash N Tree FACW FRLA8 Fraxinus dipetela Ash N Tree FACW FRDI29 Juglans californica var. californica Southern California Walnut N Tree FAC JUCA10 Juglans regia Persian or English Walnut E Tree FAC JURE*11 Morus alba Fruitless Mulberry E Tree MOAL12 Pinus sabiniana Grey Pine, Foothill Pine E Tree PISA213 Platanus racemosa Western Sycamore N Tree PLRA14 Populus fremontii Fremont Cottonwood N Tree FACW POFR215 Quercus douglasii Blue Oak N Tree QUDO16 Quercus lobata Valley Oak, Roble Oak N Tree FAC QULO17 Quercus lobata x douglasii N Tree QULXD*18 Quercus wislizenii var. wislizenii Interior Live Oak Tree form N Tree QUWIW19 Robinia pseudoacacia Black Locust E Tree FAC ROPS20 Salix babylonica Weeping Willow E Tree OBL SABA221 Salix gooddingii Goodding s Black Willow N Tree OBL SAGO22 Salix laevigata Red Willow N Tree OBL SALA*23 Salix lucida ssp. lasiandra Pacific Willow N Tree OBL SALUL24 Tamarix sp. Tamarisk IE Tree TASP*25 Acer saccharinum Silver Maple E Tree ACSA*26 Catalpa bignoniodes Catalpa E Tree CABI*27 Ulmus americana American Elm E Tree ULAM*28 Cephalanthus occidentalis var. californicus Button Bush N Shrub OBL CEOCC229 Ficus carica Edible Fig IE Shrub UPL FICA30 Lupinus sp. Bush Lupine N Shrub UPL LUSP*31 Nicotiana glauca Tree Tobacco E Shrub FAC NIGL32 Salix exigua Narrow-Leaved Willow IN Shrub OBL SAEX33 Salix lasiolepis Arroyo Willow N Shrub OBL SALA634 Salix melanopsis Dusky Willow N Shrub OBL SAME235 Sambucus mexicana Blue Elderberry N Shrub FAC SARA2TUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDOR

215Scientific Name Common Name Locality Habit USFWS Hydric Code SCS Code36 Toxicodendron diversiloba Poison Oak N Shrub TODI37 Rhamnus californica ssp. californica California Coffeeberry N Shrub RHCACA38 Vitis californica California Grape N Vine FACW VICA539 Convolvulus arvensis Bindweed, Orchard Morning Glory IE Vine COAR440 Cucurbita palmata Coyote Melon N Vine CUPA41 Rubus ursinus California Blackberry N Vine RUUR42 Rubus discolor Himalayan Berry IE Herb RUDI243 Rubus leucodermis Black Cap Raspberry N Herb RULE44 Artemisia douglasiana Mugwort N Herb FACW ARDO345 Baccharis salicifolia Mule fat, Seep willow, Water wally N Herb FACW BASA446 Centaurea solstitialis Yellow Star Thistle IE Herb CESO347 Chamaesyce albomarginata Rattlesnake Spurge N Herb CHAL1148 Chenopodium album Pig weed, lambs quarters IE Herb FAC CHAL749 Datura wrightii Jimson Weed N Herb DAWR250 Epilobium sp. Willow Herb N Herb EPSP*51 Gallium aparine Goose Grass N Herb FACU GAAP252 Gnaphalium sp. Everlasting N Herb GNSP*53 Helianthus annuus Sun Flower N Herb FAC HEAN354 Mentzelia sp. Blazing Star N Herb MESP*55 Mimulus guttatus Monkey Flower N Herb OBL MIGU56 Phytolacca americana Pokeweed, Pokeberry, Pigeon Berry E Herb PHAM457 Plantago sp. Plantain E Herb FACW PLSP*58 Polygonum hydropiperoides Waterpepper N Herb OBL POHY259 Rumex crispus Curly Dock E Herb FACW RUCR60 Urtica dioica ssp. holosericea Hoary Nettle N Herb FACW URDIH61 Xanthium strumarium Common Cocklebur N Herb FAC+ XAST62 Brassica nigra Black Mustard E Herb BRNI63 Conium maculatum Poison Hemlock E Herb COMA264 Eremocarpus setigerus Turkey Mullien N Herb ERSE365 Melilotus alba White Sweet Clover IE Herb MEAL266 Melilotus officinalis Yellow Sweet Clover IE Herb MEOF67 Oenothera elata ssp hirsutissima Evening Primrose N Herb OEELH68 Osmorhiza brachypoda California Sweetcicely N Herb OSBR69 Oxalis corniculata Oxallis IE Herb OXCO70 Plantago major Common Plantain N Herb PLMA2APPENDIX BAPPENDIX B

APPENDIX B216Scientific Name Common Name Locality Habit USFWS Hydric Code SCS Code71 Ricinus communis Castor Bean E Herb RICO*72 Solanum americanum Nightshade N Herb SOAM73 Verbascum blattaria Moth Mullien IE Herb VEBL74 Verbascum thapsus Mullien N Herb VETH75 Vicia americana American Vetch N Herb FACU VIAM76 Arundo donax Giant Reed IE Grass ARDO477 Avena fatua Wild Oat IE Grass AVFA78 Bromus sp. IE Grass BRSP*79 Bromus tectorum Cheat Grass E Grass BRTE80 Cynodon dactylon Bermuda Grass IE Grass FAC CYDA81 Echinochloa crus-galli IE Grass ECCR82 Paspalum dilatatum Dallis Grass IE Grass FAC PADI383 Polypogon maritimus Beard Grass IE Grass FACW POMA1084 Setaria pumila IE Grass SEPU885 Adiantum jordanii California Maidenhair fern N Fern ADJO86 Selaginella hansenii Spike Moss N Fern SEHA287 Pentagramma triangularis Golden Backed Fern N Fern PETR788 Woodwardia fimbrata Giant Chain Fern N Fern WOFI89 Cuscuta sp Dodder IN Parasite CUSP*90 Phorodendron macrophyllum Poplar Mistletoe N Parasite PHMA1891 Carex sp. N Em Herb CASP*92 Ceratophyllum demersum Hornwort, Common coon s tail N Em Herb OBL CEDE493 Egeria densa Brazilian Waterweed IE Em Herb OBL EGDE94 Eichhornia crassipes Water Hyacinth IE Em Herb OBL EICR95 Eleocharis sp. Spike Rush N Em Herb ELSP*96 Elodea canadensis Common Waterweed N Em Herb OBL ELCA797 Juncus effusus N Em Herb OBL JUSP*98 Lemna minor Duckweed N Em Herb OBL LEMI399 Ludwigia repens Water Primrose N Em Herb OBL LURE2100 Myriophyllum aquaticum Parrots Feather IE Em Herb OBL MYAQ2101 Myriophyllum hippuroides Western Milfoil N Em Herb OBL MYHI102 Potamogeton crispus Crispate-Leaved Pondweed IE Em Herb OBL POCR3103 Scirpus acutus var. occidentalis Tule N Em Herb OBL SCACO104 Typha latifolia Broad-Leaved Cattail IN Em Herb OBL TYLA105 Hydrocotyle verticillata IE Em Herb OBL HYVE2106 Equisetum arvense Common Horsetail IN Em Fern FAC EQARTUOLUMNE RIVER TECHNICAL ADVISORY COMMITTEEHABITAT RESTORATION PLAN FOR THE LOWER TUOLUMNE RIVER CORRIDORCommon names and taxonomy are taken from Hickman, (1993). The scientific name is followed by: (N) for native, (IN)for invasive native, (E) for exotic, and (IE) for invasive exotic. The SCS codes are taken from the soil conservation service index.SCS codes that are followed an asterix are plants for which there was no found code.


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