Biological Opinions - Bureau of Reclamation

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Scarnecchia, D. L. 1981. Effects of streamflow and upwelling on yield of wild coho salmon (Oncorhynchus kisutch). Can. J. Fish. Aquatic Sci. 38:4.71-475. Scheiff, T. and P. Zedonis. 2011. The influence of Lewiston Dam releases on water temperatures of the Trinity and Klamath rivers, California. April to October, 2010. Arcata Fisheries Data Series Report Number DS 2011-22. U. S. Fish and Wildlife Service, Arcata Fish and Wildlife Office, Arcata, California. Schlosser, I. J. 1985. Flow regime, juvenile abundance, and the assemblage structure of stream fishes. Ecology 66: 1484–1490. Shaffer, M.L. 1981. Minimum population sizes for species conservation. BioScience 31:131-134 Sharr, S., C. Melcher, T. Nickelson, P. Lawson, R. Kope, and J. Coon. 2000. 2000 review of amendment 13 to the Pacific Coast salmon plan. Exhibit B.3.b. OCN workgroup report. Pacific Fisheries Management Council, Portland, OR. Shulenburger, L., Y.C. Lai, T. Yalcinkaya, and R.D. Holt. 1999. Controlling transient chaos to prevent species extinction. Physics Letters A 260, 156–161. Sigler, J.W., Bjornn, T.C., and Everest, F.H. 1984. Effects of chronic turbidity on density and growth of steelheads and coho salmon. Trans. Am. Fish. Soc. 113: 142–150. Simondet, J. A. 2006. Expert testimony provided for trial-type hearing: Matter of the Klamath Hydroelectric Project (License Applicant PacifiCorp), Docket Number 2006-NMFS- 0001, FERC Project Number 2082. Final Ruling dated September 27, 2006. Sinnott, S. 2010. 2009 Klamath River datasonde report. Final Report. Prepared by Yurok Tribe Environmental Program, Klamath, California. Sinnott, S. 2011. 2010 Klamath River nutrient summary report. Final Report. Prepared by Yurok Tribe Environmental Program, Water Division, Klamath, California. Six Rivers National Forest Watershed Interaction Team. 1999. FishXing software, version 2.2 Snyder DT, and Morace JL. 1997. Nitrogen and phosphorus loading from drained wetlands adjacent to Upper Klamath and Agency Lakes, Oregon. Water-Resources Investigations Report 97-4059. U.S. Department of the Interior, U.S. Geological Survey, Denver, Colorado in cooperation with the Bureau of Reclamation. Snyder, J. 0. 1931. Salmon of the Klamath River, California. Calif. Department of Fish and Game Fisheries Bulletin No. 34. Spalding, S., Peterson, N.P., and Quinn, T.P. 1995. Summer distribution, survival and growth of juvenile coho salmon, Oncorhynchus kisutch, under varying experimental conditions of brushy instream cover. Trans. Am. Fish. Soc. 124: 124.130. 469
Sommer, T. R., M. L. Nobriga, W. C. Harrel, W. Batham, and W. J. Kimmerer. 2001. Floodplain rearing of juvenile Chinook salmon: evidence of enhanced growth and survival. Canadian Journal of Fisheries and Aquatic Sciences. 58:325–333. Sommer, T.R., W.C. Harrell, A.M. Solger, B. Tom, and W. Kimmerer, 2004. Effects of Flow Variation on Channel and Floodplain Biota and Habitats of the Sacramento River, California, USA. Aquatic Conservation-Marine and Freshwater Ecosystems 14:247-261. Soto, T. 2012. Spreadsheet of 2002-11 juvenile fish presence-absence in Middle Klamath Tributaries. Karuk Tribe of California. Soto, T., A. Corum, H. Voight, D. Hillemeier, and L. Lestelle. 2008. The role of the Klamath River mainstem corridor in the life history and performance of juvenile coho salmon (Oncorhynchus kisutch). Phase I Report 2006-07 Winter. Prepared for Bureau of Reclamation Mid-Pacific Region, Klamath Area Office. Spence, B. C., G. A. Lomnicky, R. M. Hughes, and R. P. Noviztki. 1996. An ecosystem approach to salmonid conservation. TR-4501-96-6057. ManTech Environmental Research Services Corp., Corvallis, Oregon. Copy available at: http://www.nwr.noaa.gov/Publications/Reference-Documents/ManTech-Report.cfm Stearns, S. C. 1992. The evolution of life histories. New York, New York, Oxford University Press. Stewart, I. T., D. R. Cayan, and M. D. Dettinger. 2005. Changes toward earlier streamsflow timing across western North America. Journal of Climate 18: 1136-1155. Stocking, R. W. and J. L. Bartholomew. 2007. Distribution and habitat characteristics of Manayunkia speciosa and infection prevalence with the parasite Ceratomyxa shasta in the Klamath River, Oregon-California. J. Parasitol. 93: 78-88. Stout, H.A., P.W. Lawson, D. Bottom, T. Cooney, M. Ford, C. Jordan, R. Kope, L. Kruzic, G.Pess, G. Reeves, M. Sheuerell, T. Wainwright, R. Waples, L. Weitkamp, J. Williams and T. Williams. 2010. Scientific conclusions of the status review for Oregon Coast coho salmon (Oncorhynchus kisutch). Draft report from the Biological Review Team. Northwest Fisheries Science Center, Seattle, Washington. May 20, 2010. Strange, J.S. 2008. Personal communication. Fish biologist. Yurok Tribal Fisheries Program. Weitchpec, CA. Strange, J.S. 2010a. Salmonid use of thermal refuges in the Klamath River: 2009 annual monitoring results. Yurok Tribal Fisheries Program. Weitchpec, CA. Strange, J. 2010b. Investigating the apparent absence of polychaetes (Manayunkia speciosa) in the Shasta River: distribution of vectors for myxozoan fish diseases. Yurok Tribal Fisheries Program. March. Hoopa, CA. 470
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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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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,
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
Page 441 and 442: Miller, R.R., and G.R. Smith. 1981.
Page 443 and 444: Perkins, D.L., and G.G. Scoppettone
Page 445 and 446: (Deltistes luxatus) in Tule and Cle
Page 447 and 448: Terwilliger, M. 2006. Physical habi
Page 449 and 450: USBR [U.S. Bureau of Reclamation].
Page 451 and 452: Williams, J.E. 2000. Chapter 13. Th
Page 453 and 454: Arthington, A.H., S.E. Bunn, N.L. P
Page 455 and 456: Beeman, J., S. Juhnke, G. Stutzer a
Page 457 and 458: Brommer, J.E. 2000. The evolution o
Page 459 and 460: Department of the Army Regional Gen
Page 461 and 462: Chilcote, M. W. 2003. Relationship
Page 463 and 464: Dunsmoor LK, and Huntington CW. 200
Page 465 and 466: Foott, J.S., R. Stone, E. Wiseman,
Page 467 and 468: Habera, J.W., R.J. Strange, B.D. Ca
Page 469 and 470: Hemstreet, T. 2013. Electronic mail
Page 471 and 472: Jordan, M. S. 2012. Hydraulic predi
Page 473 and 474: Kostow, K. E., A. R. Marshall and S
Page 475 and 476: MacFarlane, R. B., S. Hayes, and B.
Page 477 and 478: Moyle, P. B. 2002. Inland Fishes of
Page 479 and 480: PacifiCorp Klamath Hydroelectric Pr
Page 481 and 482: Oregon Department of Environmental
Page 483 and 484: Puckridge, J. T., F. Sheldon, K. F.
Page 485: Ring, T.E. and B. Watson. 1999. Eff
Page 489 and 490: Taylor, R. 1991. A review of local
Page 491 and 492: USFWS [U. S. Fish and Wildlife Serv
Page 493 and 494: Ward G, and Armstrong N. 2010. Asse
Page 495 and 496: Winker, K., J. H. Rappole, and M. A
Page 497 and 498: 77 FR 476. National Marine Fisherie
Page 499 and 500: UKL Elevation (feet) Active Storage
Page 505 and 506: 16.2 Appendix B: Elevation Flow Dat
Page 507 and 508: 490
Page 509 and 510: Week of Water Year 1981 1982 1983 1
Page 527 and 528: Water Year October November Decembe
Page 533 and 534: 16.3 Appendix C: Description of Res
Page 535 and 536: 4. Removal of Small Dams (permanent
Page 537 and 538:
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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