Biological Opinions - Bureau of Reclamation

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Figure 3.2. Location of the Project in the Upper Klamath River Basin of Oregon and California (Reclamation 2013a). 9
4 PROPOSED ACTION Reclamation proposes to continue to operate the Project to store, divert, and convey water to meet authorized Project purposes and contractual obligations in compliance with applicable State and Federal law. Reclamation also proposes to carry out the activities necessary to maintain the Project and ensure its proper long-term functions and operation. The period covered by this proposed action is the signature date of this BiOp through March 31, 2023. Reclamation’s proposed Project operations from 2013 to 2023 consist of three major elements: 1. Store waters of the Klamath and Lost Rivers. 2. Operate the Project, or direct the operation of the Project, for the delivery of water for irrigation purposes, subject to water availability, while maintaining lake and river hydrologic conditions that avoid jeopardizing the continued existence of listed species and adverse modification of designated critical habitat. 3. Perform operation and maintenance (O&M) activities necessary to maintain Project facilities to ensure proper long-term function and operation. Each of the elements of the proposed action is described in greater detail in the following sections. Elevations used in this section are referenced to Reclamation’s datum for the upper Klamath Basin, which is 1.78 feet higher than the National Geodetic Vertical Datum of 1929. 4.1 Element One Store waters of the Klamath and Lost Rivers. 4.1.1 Annual Storage of Water Reclamation plans to store water annually in UKL, Clear Lake, and Gerber Reservoir. The majority of inflow occurs from November through May. In some years of high net inflows or atypical inflow patterns, contributions to the total volume stored can also be significant in October and June. The majority of water delivery from storage occurs during April through September, although limited delivery occurs in March, October, and November. Storing water through the winter and spring results in peak lake and reservoir storage between March and May. The Klamath Project’s primary storage reservoir, UKL, is shallow and averages only about 6 feet (ft) (1.8 meters [m]) of usable storage when at full pool (approximately 515,000 acre-feet). Clear Lake and Gerber Reservoir also have limited storage capability. Thus, UKL, Clear Lake, and Gerber Reservoir do not have the capacity to carry over significant amounts of stored water from one year to the next. UKL also has limited capacity to store higher than normal inflows during spring and winter months, because the levees surrounding parts of UKL are not adequately constructed or maintained for that purpose. Therefore, the amount of water stored in any given year is highly dependent on net inflows in that year, and in preceding years. Inflow throughout the irrigation season is predominantly dependent upon snowpack to sustain flows during the summer and fall months. Ground water is an important component of inflow to UKL and also 10
Page 1 and 2: National Marine Fisheries Service U
Page 3 and 4: 7.4.5 LRS and SNS Population Dynami
Page 5 and 6: 11.1.5 Critical Assumptions .......
Page 7 and 8: 16 APPENDICIES ....................
Page 9 and 10: Table 8.2 UKL end-of-month elevatio
Page 11 and 12: LIST OF FIGURES Figure 3.1. The act
Page 13 and 14: Figure 11.17. Coho salmon fry habit
Page 15 and 16: ABBREVIATIONS AND ACRONYMS Abbrevia
Page 17 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: Figure 3.1. The action area for Rec
Page 29 and 30: 4.2 Element Two Operate the Project
Page 31 and 32: October 1 and March 1. The proposed
Page 33 and 34: Reclamation incorporated the 1981 t
Page 35 and 36: Provide Project irrigation deliveri
Page 37 and 38: Table 4.3. UKL fill rate adjustment
Page 39 and 40: Table 4.5. Calculation of fall/wint
Page 41 and 42: Flows below IGD are ultimately the
Page 43 and 44: The EWA, Project Supply, and UKL Re
Page 45 and 46: Table 4.8. Environmental Water Acco
Page 47 and 48: eleases somewhat on the ascending l
Page 49 and 50: fish disease, die off, entrainment,
Page 51 and 52: acre-feet when the Project Supply c
Page 53 and 54: Table 4.11. Monthly maximum Lower K
Page 55 and 56: 4.2.4 Ramp-Down Rates at Iron Gate
Page 57 and 58: progresses and EWA volumes are upda
Page 59 and 60: O&M activities are carried out eith
Page 61 and 62: 1. The A Canal has six headgates th
Page 63 and 64: Therefore, Reclamation proposes to
Page 65 and 66: coordinate with the NMFS to develop
Page 67 and 68: the confluence with Omogar Creek at
Page 69 and 70: though several major improvements t
Page 71 and 72: Sucker larvae transform into age-0
Page 73 and 74: units: (1) Clear Lake; (2) Tule Lak
Page 75 and 76: 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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