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1 INTRODUCTION This document transmits the concurrence determinations and biological opinions (BiOp) of the U.S. Fish and Wildlife Service (USFWS) and the National Marine Fisheries Service (NMFS; collectively, the “Services” or “we”), based on our review of the proposed operations of the Klamath Project (Project) by the Bureau of Reclamation (Reclamation) in Klamath County in Oregon and Siskiyou and Modoc Counties in California. Table 1.1 displays the Federally-listed species (hereafter referred to as listed species) and critical habitats considered in this document. This document was prepared in accordance with section 7 of the Endangered Species Act of 1973, as amended (ESA; 16 U.S.C. § 1531 et seq.). Reclamation’s request for formal consultation was received by the USFWS and the NMFS on December 3, 2012. Table 1.1. Listed species and critical habitats considered in this document. Scientific name Common name Listing Critical habitat Chasmistes brevirostris shortnose sucker (SNS) Endangered Yes Deltistes luxatus Lost River sucker (LRS) Endangered Yes Acipenser medirostris Southern Distinct Population Segment (DPS) green sturgeon Threatened No Oncorhynchus kisutch Southern Oregon/Northern California Coast (SONCC) coho salmon Evolutionarily Threatened Yes Significant Unit (ESU) Thaleichthys pacificus Southern DPS eulachon Threatened Yes This BiOp and the concurrence determinations are based on information provided in Reclamation’s Final Biological Assessment (BA; Reclamation 2012) and other sources of information. A complete record of this consultation is on file at the NMFS Northern California office in Arcata, California, and at the USFWS office in Klamath Falls, Oregon. 2 BACKGROUND AND CONSULTATION HISTORY 2.1 Background The Klamath Basin’s hydrologic system currently consists of a complex of interconnected rivers, canals, lakes, marshes, dams, diversions, wildlife refuges, and wilderness areas. Alterations to the natural hydrologic system began in the late 1800s and expanded in the early 1900s, including water diversions by private water users, Reclamation’s Project, and several hydroelectric dams operated by a private company, currently known as PacifiCorp. PacifiCorp’s Klamath Hydroelectric Project (KHP) was constructed between 1911 and 1962, and includes eight developments: (1) East and (2) West Side power facilities at Link River Dam; (3) Keno Dam; (4) J.C. Boyle Dam; (5) Copco 1 Dam; (6) Copco 2 Dam; (7) Fall Creek Dam; and (8) Iron Gate Dam (IGD). The Link River Dam and Upper Klamath Lake (UKL) are not part of the KHP. PacifiCorp operated the KHP under a 50-year license issued by the Federal Energy Regulatory Commission (FERC) until the license expired in 2006. PacifiCorp continues to operate the KHP under annual licenses based on the terms of the previous license. 1
In 2001, the Services issued BiOps on the effects of Reclamation’s Project operations on listed species, and concluded that the proposed Project operations would likely jeopardize the continued existence of the Lost River sucker (LRS) and the shortnose sucker (SNS) in UKL (USFWS 2001) and the Southern Oregon/Northern California Coast (SONCC) coho salmon Evolutionarily Significant Unit (ESU) (NMFS 2001a). Because of a severe drought in 2001 and the jeopardy BiOps, Reclamation limited the volume of water delivered to Project agricultural users, and to the Lower Klamath and Tule Lake National Wildlife Refuges. In early 2002, the National Research Council (NRC) concluded that “all components of the BiOp issued by the USFWS on the endangered suckers have substantial scientific support except for the recommendations concerning minimum water levels for Upper Klamath Lake.” The NRC (2002a) “found a sound scientific basis for recommendations in the NMFS 2001 BiOp involving coordination of operations and reduction of ramping rates for flows below the mainstem dams.” However, the NRC found little scientific support for minimum mainstem flows to maintain and recover coho salmon populations. Nevertheless, the NRC did not conclude that NMFS must be wrong in its recommendations on mainstem flows that were included in the NMFS 2001 BiOp as a reasonable and prudent alternative (RPA; NRC 2002b). The NRC (2002a, 2004) also noted that Reclamation’s proposed lake and river flows, which would have caused lower mean lake levels or lower minimum river flows, lacked scientific justification. In March 2002, one month after the NRC issued its Interim Report (NRC 2002a), Reclamation finalized a new BA that covered Project operations from May 31, 2002, to March 31, 2012, and requested consultation with the NMFS and the USFWS. The USFWS issued a BiOp (finalized in May 2002) that Reclamation’s implementation of this new proposal was likely to jeopardize the continued existence of the LRS and the SNS, and provided an RPA that involved application of an adaptive management approach that still allowed for Project water deliveries. NMFS finalized a BiOp on May 31, 2002, and concluded that Reclamation’s proposed operations would likely jeopardize the continued existence of the SONCC coho salmon and would likely adversely modify critical habitat of SONCC coho salmon. In coordination with Reclamation, the NMFS’ BiOp also included a RPA that consisted of Reclamation operating the Project to ensure that IGD minimum flows increased gradually over three phases during the 10-year period of the plan for Project operations, among other additional requirements. Reclamation provided full water deliveries to irrigators in 2002 despite the continued drought. In September 2002, at least 33,000 adult salmonids died in the lowermost 40 miles of the mainstem Klamath River (CDFG 2004a, Guillen 2003, NRC 2004, Yurok Tribal Fisheries Program 2004). The fish kill was unprecedented and affected primarily Chinook salmon, although coho salmon (approximately 344), steelhead, and green sturgeon also died. The immediate cause of mortality was massive infections of Ichthyopthirius multifilis (ich) and the bacterial pathogen Flavobacter columnare (columnaris; CDFG 2003, Guillen 2004a, NRC 2004, Yurok Tribal Fisheries Program 2004). Several fisheries groups, environmental organizations, and tribes filed suit against Reclamation and the NMFS in Federal district court, alleging violations of the ESA. The district court overturned a significant aspect of the RPA, finding the requirement that Reclamation provide only 57 percent of the long-term flows to be arbitrary and capricious. The issue on appeal was the district court’s determination that Phases I and II of the RPA, or the short term measures, 2
Page 1 and 2: National Marine Fisheries Service U
Page 3 and 4: 7.4.5 LRS and SNS Population Dynami
Page 5 and 6: 11.1.5 Critical Assumptions .......
Page 7 and 8: 16 APPENDICIES ....................
Page 9 and 10: Table 8.2 UKL end-of-month elevatio
Page 11 and 12: LIST OF FIGURES Figure 3.1. The act
Page 13 and 14: Figure 11.17. Coho salmon fry habit
Page 15 and 16: ABBREVIATIONS AND ACRONYMS Abbrevia
Page 17: Abbreviation/Acronym YTEP WDFW WRIM
Page 21 and 22: Findings of Fact and Order of Deter
Page 23 and 24: proposed changes to the vegetation
Page 25 and 26: Figure 3.1. The action area for Rec
Page 27 and 28: 4 PROPOSED ACTION Reclamation propo
Page 29 and 30: 4.2 Element Two Operate the Project
Page 31 and 32: October 1 and March 1. The proposed
Page 33 and 34: Reclamation incorporated the 1981 t
Page 35 and 36: Provide Project irrigation deliveri
Page 37 and 38: Table 4.3. UKL fill rate adjustment
Page 39 and 40: Table 4.5. Calculation of fall/wint
Page 41 and 42: Flows below IGD are ultimately the
Page 43 and 44: The EWA, Project Supply, and UKL Re
Page 45 and 46: Table 4.8. Environmental Water Acco
Page 47 and 48: eleases somewhat on the ascending l
Page 49 and 50: fish disease, die off, entrainment,
Page 51 and 52: acre-feet when the Project Supply c
Page 53 and 54: Table 4.11. Monthly maximum Lower K
Page 55 and 56: 4.2.4 Ramp-Down Rates at Iron Gate
Page 57 and 58: progresses and EWA volumes are upda
Page 59 and 60: O&M activities are carried out eith
Page 61 and 62: 1. The A Canal has six headgates th
Page 63 and 64: Therefore, Reclamation proposes to
Page 65 and 66: coordinate with the NMFS to develop
Page 67 and 68: the confluence with Omogar Creek at
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though several major improvements t
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Sucker larvae transform into age-0
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units: (1) Clear Lake; (2) Tule Lak
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Figure 7.2. Adult spawning populati
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Table 7.1. Estimated LRS and SNS ad
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1905, Ch. 567, 33 Stat. 714). The P
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Figure 7.4 Modeled April through No
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7.9.2 Klamath Basin The Oregon Clim
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A change in mean precipitation rang
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Table 7.2 Impaired water bodies wit
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Table 7.3 Seasonal comparisons of p
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ammonia that is lethal to 50 percen
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Table 7.4 Estimated external phosph
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examination of juvenile suckers fro
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Evaluation of baseline hydrology in
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2012 1931 through 2012 12.6% 0.24 5
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The overall water year trend (Table
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Figure 7.7 Sprague River trends, wa
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Figure 7.9 Sprague River trends, wa
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Figure 7.12 Williamson River trends
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Figure 7.14 UKL trends, water years
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Figure 7.17 UKL: net inflow departu
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7.10.3.3 Competition and Predation
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By late July, surviving larval suck
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Threat Nature of Threat Life Stage
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2011) and increased adult spawning
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Based on the best available informa
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contrast, water levels began 1.5 ft
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evaporation and seepage estimated a
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prolonged low oxygen conditions if
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The April through September 4,034.6
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8 EFFECTS OF THE ACTION ON LOST RIV
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Although the volume of Project wate
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than 1 m), and fitting one or more
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Figure 8.3. UKL elevations at the e
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Services and Reclamation will deter
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For cumulative net inflow values be
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Figure 8.8. UKL elevations at the e
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Figure 8.10. UKL elevations at the
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Figure 8.12. UKL elevations at the
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natural and man-caused changes in i
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Table 8.1 UKL end-of-month surface
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UKL. Based on best available inform
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larvae in UKL. Annual production of
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Table 8.5 UKL end-of-month elevatio
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Based on our review of the literatu
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into the Pelican Bay water quality
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We assume that UKL surface elevatio
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vary by several orders of magnitude
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survival rates, we know that some o
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populations, and contains the large
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8.3.5.1 Effects to Adult Sucker Spa
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Table 8.8 Clear Lake surface elevat
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occur, especially in the west lobe.
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Table 8.9 End of the month surface
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8.3.7.4 Effects of Entrainment Loss
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The source of the sediment is unkno
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period when they migrate upstream t
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limited LRS and SNS persistence in
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term and localized and because fish
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8.5.1 Canal Salvage Reclamation pro
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high predation rates and failure of
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include the Klamath Basin Rangeland
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Figure 9.1 Designated CHUs for the
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These are discussed in greater deta
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The proposed action will have no ef
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No other spawning habitat exists be
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consulted on. Current monitoring da
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proposed action and this PCE suppor
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Because of a multi-decade lack of r
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Adverse effects of the proposed act
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that juvenile survival is most like
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elocation effort in Lake Ewauna to
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LRS and SNS population resiliency o
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stratum 4 (Interior Klamath) in whi
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Pacific salmonids Oncorhynchus spp.
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scenario, actions and elements of t
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flow prescriptions should mimic pro
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11.2.1 Current Condition of Critica
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11.2.2 Factors Affecting SONCC Coho
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e disoriented or displaced downstre
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enhancement, and rehabilitative act
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Water Temperature Sedimentation Org
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Figure 11.1 Longitudinal and season
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functioning floodplains that fail t
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downstream of IGD, (2) enhance coho
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few local ranchers and water distri
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in some tributaries, access to and
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11.3.7 Summary of Critical Habitat
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these two time periods, the effects
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consists of approximately 29,000 ac
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The PacifiCorp habitat conservation
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IGD, or used in constructed habitat
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estoration, watershed planning, sal
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Table 11.4. Modeled suspended sedim
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parasites Ceratomyxa shasta (causes
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that become infected is estimated t
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where snow water equivalent is proj
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minimizing disease risks, the detai
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Figure 11.4. Proposed action, histo
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Figure 11.6. Proposed action weekly
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Figure 11.9. Regression between EWA
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Figure 11.11. Proposed action and o
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Figure 11.12. Number of days per wa
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Figure 11.14. Monthly coefficient o
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IGD. The proposed action modeled da
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The results from Table 11.7 indicat
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likely to increase the quantity of
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habitat decreases between the Shast
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Table 11.9. Daily average mainstem
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Table 11.10. Daily average mainstem
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5% 3336 13176 27664 26168 30946 237
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The proposed action results in agri
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Figure 11.21. Monthly mean of daily
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Riparian restoration projects will
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expected to be typical riparian spe
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Table 11.13. Annual percent of proj
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esource needs as they grow, and 3)
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11.5.2 Klamath River Basin Adjudica
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coho salmon within the Klamath Rive
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aspects of a natural flow regime th
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element of coho salmon critical hab
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12.1.1.1 Risk Analyses for Endanger
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ESU DIVERSITY STRATA POPULATIONS IN
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eproduction, and distribution. The
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Figure 12.2. Historic population st
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the average ratio of IP-km to total
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Although long-term data on coho sal
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1980 1981 1982 1983 1984 1985 1986
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maintain viable abundances in many
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12.2.5.5 Viability Summary Though p
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coastal currents and upwelling, kno
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12.2.6.2 Marine Derived Nutrients M
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fisheries south of Cape Falcon, Ore
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12.3 Environmental Baseline of Coho
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water temperatures up to 19 ºC in
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some coho salmon smolts may stop mi
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threshold, all Klamath River coho s
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abundance threshold (Table 12.3). T
Page 347 and 348:
mainstem Klamath and Trinity rivers
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Although there are risks to Klamath
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activities are generally beneficial
Page 353 and 354:
12.4 Effects to Individuals The pro
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12.4.1.2 Response 12.4.1.2.1 Adults
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(2012) believes is representative o
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genotype II density of 5 spores/L w
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flows provide a limit to the increa
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polychaete and sediment disturbance
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which will likely result in a relat
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etween Trees of Heaven (RM 172) and
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action. Reclamation estimated that
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Based on literature, increased comp
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Table 12.6. Summary of risks result
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most juveniles. Stream flow diversi
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at most fish relocation sites, base
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higher, the minimally increased sed
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Small pulses of moderately turbid w
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Boulder faces in the deflector stru
Page 385 and 386:
conditions may fail if those condit
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Adverse effects of the proposed act
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Potential Stressor Habitat Reductio
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Potential Stressor Elevated water t
Page 393 and 394:
12.6.2 Effects of fitness consequen
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13 INCIDENTAL TAKE STATEMENT Sectio
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Table 13.1 Summary of maximum annua
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in fewer larvae and juveniles, and
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Table 13.2 Estimated annual maximum
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1.2.1.8. Incidental Take Caused by
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characteristics of aquatic species,
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Table 13.5 Expected annual Environm
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Cause of Incidental Take Habitat Re
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Clear Lake, Gerber Reservoir, and T
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This term and condition is requirin
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13.4 Mandatory Monitoring and Repor
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Required hydrologic monitoring incl
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Table 13.7. Summary of LRS and SNS
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T&C or Mandatory Monitoring Mandato
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Table 13.9 Summary of reporting and
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Table 13.10 Summary of meetings req
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the above QA/QC procedures describe
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Barry, P.M., E.C. Janney, D.A. Hewi
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Burdick, S.M. and J. Rasmussen. 201
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Dunsmoor, L., L. Basdekas, B. Wood,
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Garen, D. 2011, Upper Klamath Basin
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Janney, E.C., B.S. Hayes, D.A. Hewi
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Laenen, A., and A.P. LeTourneau. 19
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Miller, R.R., and G.R. Smith. 1981.
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Perkins, D.L., and G.G. Scoppettone
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(Deltistes luxatus) in Tule and Cle
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Terwilliger, M. 2006. Physical habi
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USBR [U.S. Bureau of Reclamation].
Page 451 and 452:
Williams, J.E. 2000. Chapter 13. Th
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Arthington, A.H., S.E. Bunn, N.L. P
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Beeman, J., S. Juhnke, G. Stutzer a
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Brommer, J.E. 2000. The evolution o
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Department of the Army Regional Gen
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Chilcote, M. W. 2003. Relationship
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Dunsmoor LK, and Huntington CW. 200
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Foott, J.S., R. Stone, E. Wiseman,
Page 467 and 468:
Habera, J.W., R.J. Strange, B.D. Ca
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Hemstreet, T. 2013. Electronic mail
Page 471 and 472:
Jordan, M. S. 2012. Hydraulic predi
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Kostow, K. E., A. R. Marshall and S
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MacFarlane, R. B., S. Hayes, and B.
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Moyle, P. B. 2002. Inland Fishes of
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PacifiCorp Klamath Hydroelectric Pr
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Oregon Department of Environmental
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Puckridge, J. T., F. Sheldon, K. F.
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Ring, T.E. and B. Watson. 1999. Eff
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Sommer, T. R., M. L. Nobriga, W. C.
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Taylor, R. 1991. A review of local
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USFWS [U. S. Fish and Wildlife Serv
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Ward G, and Armstrong N. 2010. Asse
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Winker, K., J. H. Rappole, and M. A
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77 FR 476. National Marine Fisherie
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UKL Elevation (feet) Active Storage
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16.2 Appendix B: Elevation Flow Dat
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490
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Week of Water Year 1981 1982 1983 1
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Water Year October November Decembe
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16.3 Appendix C: Description of Res
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4. Removal of Small Dams (permanent
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Information regarding consideration
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9. Piping Ditches a. Project Descri
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. Site-Specific Restrictions Restri
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6. Protection Measures The followin
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to enter or be placed where they co
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shall be distributed throughout the
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weed free straw, silt fences) are i
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the project is located, and compris
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2. Post Construction Monitoring and
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Median Seasonal Flow (acre-feet) Me
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Median Seasonal Net Inflow (acre-fe
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16.5 Appendix E: Observed and Model
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Observed and modeled proposed actio
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Observed and modeled proposed actio
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16.6 Appendix F: Analyzing the rela
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Table 1. Paired comparison of the c
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Table 3. The difference in the mean
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