Biological Opinions - Bureau of Reclamation

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12.6 Integration and Synthesis ............................................................................................ 367 12.6.1 Effects of the proposed action to the Interior Klamath Stratum populations ......... 369 12.6.2 Effects of fitness consequences on population viability parameters ...................... 376 12.6.3 Summary ................................................................................................................. 377 12.7 Conclusion .................................................................................................................. 377 13 INCIDENTAL TAKE STATEMENT ................................................................................ 378 13.1 Assumptions ................................................................................................................ 378 13.1.1 Lost River and Shortnose Suckers .......................................................................... 378 13.2 Amount or Extent of Take .......................................................................................... 378 13.2.1 Lost River and Shortnose Suckers .......................................................................... 378 13.2.2 Incidental Take Summary for LRS and SNS .......................................................... 386 13.2.1 SONCC Coho Salmon ESU .................................................................................... 387 13.3 Effect of the Take........................................................................................................ 393 13.3.1 Reasonable and Prudent Measures (RPM) ............................................................. 393 13.3.2 Terms and Conditions (T&C) ................................................................................. 393 13.4 Mandatory Monitoring and Reporting Requirements under the Terms and Conditions 398 13.4.1 Lost River and Shortnose Suckers .......................................................................... 398 13.4.2 Monitoring Summary .............................................................................................. 401 13.4.3 SONCC Coho Salmon ESU .................................................................................... 405 13.5 Reporting Requirements ............................................................................................. 405 13.5.1 Lost River and Shortnose Suckers .......................................................................... 408 13.5.2 SONCC Coho Salmon ESU .................................................................................... 408 13.6 Conservation Recommendations ................................................................................ 409 13.7 USFWS Recommendations ........................................................................................ 409 13.8 NMFS Recommendation ............................................................................................ 410 14 REINITIATION NOTICE .................................................................................................. 410 15 LITERATURE CITED ....................................................................................................... 411 15.1 Sections 1 through 10, and 13 ..................................................................................... 411 15.2 Sections 11 through 13................................................................................................ 435 v
16 APPENDICIES ................................................................................................................... 481 16.1 Appendix A: Proposed Action UKL Elevation-Capacity Data .................................. 481 16.2 Appendix B: Elevation Flow Data ............................................................................. 488 16.2.1 Elevation Flow Data Charts .................................................................................... 488 16.2.2 Modeled UKL average weekly elevations (ft) for Period of Record Proposed Action Model Study 2L_MW_7_O dated December 7, 2012 ........................................................ 491 16.2.3 Modeled Link River average weekly flow (cfs) for Period of Record Proposed Action Model Study 2L_MW_7_O dated December 7, 2012 ............................................ 497 16.2.4 Modeled Klamath River at Keno average weekly flow (cfs) for Period of Record Proposed Action Model Study 2L_MW_7_O dated December 7, 2012 ............................ 501 16.2.5 Modeled Klamath River below Iron Gate Dam average weekly flow (cfs) for Period of RecordProposed Action Model Study 2L_MW_7_O dated December 7, 2012 ............ 505 16.2.6 Observed Clear Lake Reservoir end of month surface elevations in feet (Reclamation 2012). ............................................................................................................ 509 16.2.7 Observed Gerber Reservoir end of month surface elevations in feet (Reclamation 2012). 513 16.3 Appendix C: Description of Restoration Project Types ............................................. 516 16.4 Appendix D: Trend Analyses..................................................................................... 538 16.5 Appendix E: Observed and Modeled Flows .............................................................. 580 16.6 Appendix F: Analyzing the relationship of Iron Gate Dam releases on water temperature in the mainstem Klamath River during the spring .............................................. 586 vi
Page 1 and 2: National Marine Fisheries Service U
Page 3 and 4: 7.4.5 LRS and SNS Population Dynami
Page 5: 11.1.5 Critical Assumptions .......
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 and 18: Abbreviation/Acronym YTEP WDFW WRIM
Page 19 and 20: In 2001, the Services issued BiOps
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
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progresses and EWA volumes are upda
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O&M activities are carried out eith
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1. The A Canal has six headgates th
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Therefore, Reclamation proposes to
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coordinate with the NMFS to develop
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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
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mainstem Klamath and Trinity rivers
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Although there are risks to Klamath
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activities are generally beneficial
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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
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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
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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].
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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,
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Habera, J.W., R.J. Strange, B.D. Ca
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Hemstreet, T. 2013. Electronic mail
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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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