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Table 12.4. List of projects or activities that currently have permitted or exempted take of coho salmon in the action area. Project/Activity Klamath Project Operations Yurok Tribe’s eulachon survey Habitat restoration Regional general permit for CDFW’s Fisheries Restoration Grant Program PacifiCorp habitat conservation plan Juvenile monitoring on the mainstem Klamath River Duration Action Estimated Number or Extent of Take Agency Exempted/Permitted 2010-2018 Reclamation Habitat surrogate (i.e., proportional loss of habitat availability identified in Table 19 of NMFS 2010a and decreased smolt/flow transit time identified in Table 20 in NMFS 2010a) 2011-2013 NMFS Up to 60 coho salmon juveniles/yr 2012-2017 NOAA Restoration Center 2010-2015 Corps of Engineers Up to 766* juvenile coho salmon may be annually captured, of which up to 0.6 percent of the captured coho salmon may be injured each year, and up to 0.6 percent of the captured coho salmon will be killed each year. Injury or mortality of juveniles limited to 3 percent of captured individuals and no more than 2 to 12 instream projects per HUC 10 watershed size per year. 2012-2022 PacifiCorp Habitat surrogate (i.e., habitat will be available consistent with Table 19 of the Klamath Project Operations BiOp; estimated smolt travel times will be consistent with Table 20 of the 2010 Klamath Project Operations BiOp; low dissolved oxygen concentration [
12.4 Effects to Individuals The proposed action affects SONCC coho salmon through the Project Operations and the annual restoration funding of approximately $500,000. Project Operations affect coho salmon through hydrologic and habitat modifications in the mainstem Klamath River, while the annual restoration funding affects coho salmon during restoration implementation and through habitat improvements. Note that the use of the term “proposed action” in the Project Operations section represents Klamath Project operations component of the proposed action, while the use of the term “proposed action” in the Restoration Activities section represents the habitat restoration component of the proposed action. 12.4.1 Project Operations As stated in the Effects to SONCC Coho Salmon ESU Critical Habitat section, the coho salmon effects analysis is based on the results of the formulaic approach described in the proposed action and on one element of the proposed adaptive management where details are sufficient for analysis. Besides the proposed near real-time management for minimizing disease risks, the coho salmon effects analysis does not include the proposed adaptive management because NMFS does not have sufficient information on the adaptive management approach at this time. Under the proposed action, the median Project delivery from all sources by water year is 428,200 acre-ft with a minimum of 178,000 acre-ft and a maximum of 477,000 acre-ft (Reclamation 2012). Approximately 80 percent of the Project water delivery is not returned to the mainstem Klamath River (Cameron 2013). Therefore, approximately 20 percent of the Project water is returned to the Klamath River as agricultural tailwater, which contributes to impaired water quality in the Klamath River. The proposed action’s effects to coho salmon result from the reduction to flows at IGD. 12.4.1.1 Exposure As previously discussed in the Hydrologic Effects section (i.e., section 11.4.1.1), the proposed action reduces flows in the mainstem Klamath River throughout most of the year. Therefore, all life stages of coho salmon are expected to be exposed to proposed action effects in the next ten years (Table 12.5). However, different populations of coho salmon will be exposed to varying levels of flow effects under the proposed action. Populations proximal to IGD will experience the most pronounced exposure, while populations farthest away, such as the Lower Klamath River population, are not likely to be exposed. Adult coho salmon are present in the mainstem Klamath River only during the upstream migration and spawning period. Upstream migration of adult coho salmon in the Klamath River spans the period from September to January, with peak movement occurring between late- October and mid-November. In most years, all adults are observed in tributaries prior to December 15, while in some years (e.g., Scott River in 2009) most adults are observed between December 15 and January 1. Therefore, adults that spawn in tributaries are expected to be exposed primarily in the late fall to early winter. 336
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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
Page 301 and 302: Table 11.13. Annual percent of proj
Page 303 and 304: esource needs as they grow, and 3)
Page 305 and 306: 11.5.2 Klamath River Basin Adjudica
Page 307 and 308: coho salmon within the Klamath Rive
Page 309 and 310: aspects of a natural flow regime th
Page 311 and 312: element of coho salmon critical hab
Page 313 and 314: 12.1.1.1 Risk Analyses for Endanger
Page 315 and 316: ESU DIVERSITY STRATA POPULATIONS IN
Page 317 and 318: eproduction, and distribution. The
Page 319 and 320: Figure 12.2. Historic population st
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Page 323 and 324: Although long-term data on coho sal
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Page 329 and 330: 12.2.5.5 Viability Summary Though p
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Page 333 and 334: 12.2.6.2 Marine Derived Nutrients M
Page 335 and 336: fisheries south of Cape Falcon, Ore
Page 337 and 338: 12.3 Environmental Baseline of Coho
Page 339 and 340: water temperatures up to 19 ºC in
Page 341 and 342: some coho salmon smolts may stop mi
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Page 345 and 346: abundance threshold (Table 12.3). T
Page 347 and 348: mainstem Klamath and Trinity rivers
Page 349 and 350: Although there are risks to Klamath
Page 351: activities are generally beneficial
Page 355 and 356: 12.4.1.2 Response 12.4.1.2.1 Adults
Page 357 and 358: (2012) believes is representative o
Page 359 and 360: genotype II density of 5 spores/L w
Page 361 and 362: flows provide a limit to the increa
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Page 365 and 366: which will likely result in a relat
Page 367 and 368: etween Trees of Heaven (RM 172) and
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
Page 379 and 380: higher, the minimally increased sed
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 and 390: Potential Stressor Habitat Reductio
Page 391 and 392: Potential Stressor Elevated water t
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
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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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