Biological Opinions - Bureau of Reclamation

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Potential Stressor Disease (C. shasta) Project Effects Increased likelihood of impaired growth, swimming performance, body condition, and increased stress and susceptibility to secondary infections Increased likelihood of diseaserelated mortality Life Stage Fry Parr Smolts Fry Parr, and Smolts General Time April to mid- June April to August April to June May to mid- June May to June Mainstem Location Klamathon Bridge (RM 187.6) to Orleans (RM 59) Trees of Heaven (RM 172) to Seiad Valley (RM 129) Minimization Measure(s) Flow variability will increase mainstem flows when precipitation and snow melt is occurring in the Upper Klamath Basin, which will help to dilute actinospore concentrations and/or disturb polychaetes and their habitats. In addition, flow variability will provide dynamic fluvial environments in the mainstem Klamath River that may impair polychaete fitness, reproductive success, or infection with C. shasta. Compared to observed POR conditions, the Project will increase the magnitude and frequency of peak flows, which will likely decrease the abundance of polychaetes in the spring and summer following a channel maintenance flow event. In addition, the increase in magnitude and frequency of channel maintenance flows under the proposed action will likely decrease the actinospore concentrations relative to the observed POR when the channel maintenance flow event occurs in the spring, particularly in May and June. The adaptive management element of the proposed action is likely to minimize disease risks to coho salmon during average to below average water years if EWA surplus volume is available. Lastly the proposed minimum daily flows in April to June will limit the increase in disease risks posed to coho salmon under the proposed action. Proposed Action Effects The proposed action will result in disease risks to coho salmon that are lower than observed POR conditions yet higher than under natural flow conditions. 373
Potential Stressor Elevated water temperature DO reduction Decreased outmigration rate Project Effects Increased stress Decreased swimming performance and increased stress Increased likelihood of mortality from other stressors in the mainstem Klamath River (e.g., disease, predation, impaired water quality) Life Stage Fry Parr and Smolts Parr Smolts General Time May to mid- June May to June June to August April to June Mainstem Location IGD to Scott River (RM 143) IGD (RM 190) to Orleans (RM 59) IGD (RM 190) to Shasta River (RM 176) Minimization Measure(s) Flow variability incorporated into the proposed action will likely provide increased spring flows when precipitation and snow melt is occurring in the Upper Klamath Basin, especially during wetter water years. Formulaic approach prioritizes EWA releases in the spring and minimum daily flow targets in April to June meet Hardy et al.’s (2006) recommended ecological base flows. Flow variability incorporated into the proposed action will likely provide increased summer flows when precipitation and snow melt is occurring in the Upper Klamath Basin. Increases to summer mainstem flows will likely offset some DO reductions. Flow variability incorporated into the proposed action will likely provide increased spring flows when precipitation and snow melt is occurring in the Upper Klamath Basin. Increases to mainstem flows will likely partially offset the reductions to outmigration rates. Proposed Action Effects Coho salmon will continue to have increased stress from elevated water temperatures when water daily maximum temperature become chronically above 16.5 °C in May to June Coho salmon parr will continue to have decreased swimming performance or increased stress from decreased dissolved oxygen concentration in the mainstem during the late night and early morning when dissolved oxygen concentrations are below 8.0 mg/L or 6.0 mg/L, respectively. Coho salmon smolts are likely to continue to have decreased outmigration rate in this reach, which will likely increase likelihood of decreased growth or increased mortality when environmental conditions are conducive to having increased stressors, such as increased water temperatures and disease proliferation.. 374
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National Marine Fisheries Service U
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7.4.5 LRS and SNS Population Dynami
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11.1.5 Critical Assumptions .......
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16 APPENDICIES ....................
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Table 8.2 UKL end-of-month elevatio
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LIST OF FIGURES Figure 3.1. The act
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Figure 11.17. Coho salmon fry habit
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ABBREVIATIONS AND ACRONYMS Abbrevia
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Abbreviation/Acronym YTEP WDFW WRIM
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In 2001, the Services issued BiOps
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Findings of Fact and Order of Deter
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proposed changes to the vegetation
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Figure 3.1. The action area for Rec
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4 PROPOSED ACTION Reclamation propo
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4.2 Element Two Operate the Project
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October 1 and March 1. The proposed
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Reclamation incorporated the 1981 t
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Provide Project irrigation deliveri
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Table 4.3. UKL fill rate adjustment
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Table 4.5. Calculation of fall/wint
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Flows below IGD are ultimately the
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The EWA, Project Supply, and UKL Re
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Table 4.8. Environmental Water Acco
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eleases somewhat on the ascending l
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fish disease, die off, entrainment,
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acre-feet when the Project Supply c
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Table 4.11. Monthly maximum Lower K
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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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Page 347 and 348: mainstem Klamath and Trinity rivers
Page 349 and 350: Although there are risks to Klamath
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Page 353 and 354: 12.4 Effects to Individuals The pro
Page 355 and 356: 12.4.1.2 Response 12.4.1.2.1 Adults
Page 357 and 358: (2012) believes is representative o
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Page 361 and 362: flows provide a limit to the increa
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Page 369 and 370: action. Reclamation estimated that
Page 371 and 372: Based on literature, increased comp
Page 373 and 374: Table 12.6. Summary of risks result
Page 375 and 376: most juveniles. Stream flow diversi
Page 377 and 378: at most fish relocation sites, base
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Page 381 and 382: Small pulses of moderately turbid w
Page 383 and 384: Boulder faces in the deflector stru
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Page 387 and 388: Adverse effects of the proposed act
Page 389: Potential Stressor Habitat Reductio
Page 393 and 394: 12.6.2 Effects of fitness consequen
Page 395 and 396: 13 INCIDENTAL TAKE STATEMENT Sectio
Page 397 and 398: Table 13.1 Summary of maximum annua
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Page 401 and 402: Table 13.2 Estimated annual maximum
Page 403 and 404: 1.2.1.8. Incidental Take Caused by
Page 405 and 406: characteristics of aquatic species,
Page 407 and 408: Table 13.5 Expected annual Environm
Page 409 and 410: Cause of Incidental Take Habitat Re
Page 411 and 412: Clear Lake, Gerber Reservoir, and T
Page 413 and 414: This term and condition is requirin
Page 415 and 416: 13.4 Mandatory Monitoring and Repor
Page 417 and 418: Required hydrologic monitoring incl
Page 419 and 420: Table 13.7. Summary of LRS and SNS
Page 421 and 422: T&C or Mandatory Monitoring Mandato
Page 423 and 424: Table 13.9 Summary of reporting and
Page 425 and 426: Table 13.10 Summary of meetings req
Page 427 and 428: the above QA/QC procedures describe
Page 429 and 430: Barry, P.M., E.C. Janney, D.A. Hewi
Page 431 and 432: Burdick, S.M. and J. Rasmussen. 201
Page 433 and 434: Dunsmoor, L., L. Basdekas, B. Wood,
Page 435 and 436: Garen, D. 2011, Upper Klamath Basin
Page 437 and 438: Janney, E.C., B.S. Hayes, D.A. Hewi
Page 439 and 440: 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,
Page 467 and 468:
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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