Biological Opinions - Bureau of Reclamation

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Table 2.1 Chronology of Agency Coordination Team meetings for development of Reclamation’s proposed action. Date City State May 10, 2011 Redding CA June 2-3, 2011 Medford OR June 22-23, 2011 Arcata CA July 19-20, 2011 Klamath Falls CA August 15, 2011 Teleconference September 13-14, 2011 Ashland OR October 4, 2011 Klamath Falls OR October 18, 2011 Teleconference November 8-9, 2011 Arcata CA December 6-7, 2011 Redding CA January 10-11, 2012 Redding CA February 9-10, 2012 Redding CA February 17, 2012 Teleconference February 28, 2012 Teleconference March 14, 2012 Ashland OR April 3, 2012 Teleconference April 17, 2012 Teleconference April 26-27, 2012 Medford OR May 3-4, 2012 Teleconference May 16-18, 2012 Medford OR June 4, 2012 Teleconference June 7, 2012 Teleconference June 19-20, 2012 Klamath Falls OR July24-25, 2012 Teleconference August 9, 2012 Teleconference September 21, 2012 Teleconference On December 1, 2012, Reclamation sent letters requesting initiation of formal consultation pursuant to section 7(a)(2) of the ESA. The Services received Reclamation’s request and accompanying BA on December 3, 2012. NMFS also received Reclamation’s December 21, 2012, letter clarifying the proposed minimum daily average target flows and the inclusion of a coho salmon conservation measure as part of the proposed action. The USFWS received Reclamation’s January 4, 2013, letter revising the effects determination on critical habitat for Lost River sucker and shortnose sucker, and addressing other minor points of clarification. On January 8, 2013, a letter of sufficiency of the BA was sent to Reclamation from the Services. In Section 4.3.3.5 on page 4-45 of the final BA (Reclamation 2012), Reclamation included as part of the proposed action information on mowing roads and dikes and the use of pesticides and herbicides on Project lands. The BA states the effects of these activities have been evaluated in previous ESA section 7 consultations (1-7-95-F-26 and 1-10-07-F-0056), and there are no 5
proposed changes to the vegetation and pest management activities as currently practiced. On February 8, 2013, Reclamation clarified via email that the information on pesticide use as noted in Section 4.3.3.5 was included in the BA to respond to USFWS's request to provide a complete Baseline of Project operation, and Reclamation is not requesting consultation on pesticide use as part of their request for formal consultation. Additionally, as part of their proposed action in the final BA, Reclamation included a statement that in dry years when the Project Supply is limited, it may not be possible to maintain the proposed minimum Tule Lake Sump 1A elevations because of decreased runoff and drainage from Project land. Reclamation stated in the first paragraph on page 4-38 of the BA (Reclamation 2012) that this situation is outside of their control, and Tule Lake elevations may decline to levels less than the proposed minimums and sucker relocation may be necessary. However, after finalizing the BA, Reclamation conducted further analysis on the likelihood of not meeting minimum elevations in Tule Lake. On April 9, 2013, Reclamation provided this analysis to the USFWS via email, concluding that if the Klamath Project received irrigation deliveries, the likelihood of not maintaining minimum surface elevation in Tule Lake Sump 1A was very rare. Therefore, Reclamation requested via email on April 25, 2013, that the paragraph on page 4-38 and associated Appendix 4B be removed from the proposed action and not analyzed. On May3, 2013, USFWS received Reclamation’s letter, clarifying and updating the proposed action with additional Conservation Measures. These measures included providing an additional $500,000 in FY2013 to support captive propagation; capturing and transporting listed suckers in Lake Ewauna and releasing them in UKL; and investigating the reduction of flows at Link River Dam to determine if there are feasible management options to minimize effects of entrainment at Link River Dam on larvae and juvenile listed suckers at key times when they are present at the south end of UKL. On May 7, 2013, Reclamation and NMFS met in Medford, OR to discuss several issues NMFS needed to be addressed prior to issuance of the anticipated, joint BiOps on Reclamation’s proposed action. The issues involved the minimum flows during the spring, magnitude and frequency of high flow events, and the restoration funding. On May 10, 2013, NMFS received Reclamation’s May 9, 2013, letter documenting the mutual agreement between NMFS and Reclamation to extend the consultation on the endangered southern resident killer whale DPS (Orcinus orca) for one year. On May 29, 2013, NMFS received Reclamation’s letter revising the proposed action to further minimize adverse effects of the Project on the SONCC coho salmon ESU and its critical habitat. The revised proposed action consists of: (1) increasing the minimum daily IGD flow targets for April, May, and June; (2) clarifying flexibility in operations regarding meeting minimum daily average flows downstream of IGD; (3) clarifying that the proposed action daily modeled IGD flows during high flow events will be achieved during real-time operations; (4) increasing annual fisheries habitat restoration funding to $500,000; and (5) using adaptive management for minimizing fish disease. 6
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: Findings of Fact and Order of Deter
Page 25 and 26: Figure 3.1. The action area for Rec
Page 27 and 28: 4 PROPOSED ACTION Reclamation propo
Page 29 and 30: 4.2 Element Two Operate the Project
Page 31 and 32: October 1 and March 1. The proposed
Page 33 and 34: Reclamation incorporated the 1981 t
Page 35 and 36: Provide Project irrigation deliveri
Page 37 and 38: Table 4.3. UKL fill rate adjustment
Page 39 and 40: Table 4.5. Calculation of fall/wint
Page 41 and 42: Flows below IGD are ultimately the
Page 43 and 44: The EWA, Project Supply, and UKL Re
Page 45 and 46: Table 4.8. Environmental Water Acco
Page 47 and 48: eleases somewhat on the ascending l
Page 49 and 50: fish disease, die off, entrainment,
Page 51 and 52: acre-feet when the Project Supply c
Page 53 and 54: Table 4.11. Monthly maximum Lower K
Page 55 and 56: 4.2.4 Ramp-Down Rates at Iron Gate
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
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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
Page 313 and 314:
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
Page 347 and 348:
mainstem Klamath and Trinity rivers
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Although there are risks to Klamath
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activities are generally beneficial
Page 353 and 354:
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
Page 393 and 394:
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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