Biological Opinions - Bureau of Reclamation

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Threat High pH High Water Temperatures Nature of Threat Mortality or stress and reduced productivity Mortality or stress and reduced productivity Life Stage Affected Primary Effect Mitigating Factor(s) able to avoid affected areas to some degree All life stages pH reaches >10 Unlikely to reach lethal levels and is temporary and localized, and fish can avoid affected areas Juveniles and adults mostly Temperature reaches >28 ºC Highly unlikely to reach lethal levels and is temporary and localized, and fish can avoid affected areas References Algal Toxins Parasites Disease Mortality or stress and reduced productivity Stress and reduced productivity Mortality, stress, and reduced productivity Unknown but believed to be predominantly juveniles All life stages likely affected but may have greater effect on age-0 All life stages likely affected but may have greater effect on age-0 Predation Mortality All life stages but especially 99 Some aspects studied including: presence in UKL, route of entry, presence in gut, and tissue damage consistent with known effects of microcystin Documented present for several species and effects of Neascus determined for SNS Documented present Documented present Extent of effect not known and annual variability in time and space unknown Diversity of parasites and overall effects not well known Appears to be mostly a concern when fish are highly stressed by other factors; difficult to duplicate in the lab Effects not well VanderKooi et al. 2010 Simon and Markle 2004, Simon et al. 2011, Markle et al. 2013 Foott et al. 2007 Dunsmoor and Markle
Threat Nature of Threat Life Stage Affected age-0 Primary Effect Mitigating Factor(s) documented especially at population level, but birds are known predators References 2007, Roby and Collis 2011 7.10.5 Effects of Ecosystem Restoration and Recovery Actions for the LRS and the SNS Since the early 1990s, the USFWS, Reclamation, NRCS, the State of Oregon, the Klamath Tribes, The Nature Conservancy, Klamath water users, other partners, and private landowners have been working to improve water quality and aquatic habitat conditions in the upper Klamath River Basin to support the recovery of the LRS and the SNS. Major habitat restoration efforts focusing on the endangered suckers have been completed or initiated. These include: (1) enhancement of thousands of acres of wetlands adjacent to UKL and in the watershed above the lake; (2) removal of Chiloquin Dam; (3) screening of the outlet of Clear Lake Dam; (4) construction of a new fish ladder at Link River Dam; and (5) screening of the A Canal. 7.10.5.1 Wetland Restoration in UKL The re-establishment of approximately 2,600 ac (1,050 ha) of shallow water habitat at the Williamson River Delta, which is likely to be become emergent marsh (Elseroad 2004), is expected to provide good habitat for larval suckers, and will perhaps increase survivorship and reduce vagrancy and dispersal out of UKL where survival is currently minimal (Crandall et al. 2008; Hendrixson 2008; Markle et al. 2009; Erdman et al. 2010, 2011). Monitoring has shown that larval suckers are extensively using a variety of microhabitats in the newly reconnected wetlands; they have a greater gut-fullness, and in some years are larger, than larvae in the lake (Crandall et al. 2008; Erdman and Hendrixson 2010, 2011). Additionally, restoration at the Williamson River Delta altered the path water takes when it reaches the lake, which appears to have affected the distribution of larvae, making it less likely they will be transported out of the lake (Simon et al. 2012). On the potentially negative side: in some years habitat used by larval suckers becomes dewatered by mid-July; a large number of nonnative fish, including six species that could prey on larval suckers and three that could prey on juveniles, occur in the Williamson River Delta; catch rates of age-0 suckers decline to near zero by September; and water quality in areas with deep-water emergent and transitional wetlands is poor in late summer (TNC 2009, Burdick 2012, Burdick and Hewitt 2012). Additionally, wetland habitats in the Delta provide habitat for snails that could be one source of parasitic trematodes now infecting juvenile suckers. Agency Lake Ranch and the Barnes properties (9,800 ac [4,000 ha]) along the northern and northwestern shores of Agency Lake were acquired by Reclamation and used as water storage areas, but are now managed as a part of the Upper Klamath NWR. Levees along these properties could be breached within the next 10 years; however, because of subsidence, much of the property will be too deep to maintain emergent wetland vegetation used by young suckers and 100
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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
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
Page 77 and 78: Table 7.1. Estimated LRS and SNS ad
Page 79 and 80: 1905, Ch. 567, 33 Stat. 714). The P
Page 81 and 82: Figure 7.4 Modeled April through No
Page 83 and 84: 7.9.2 Klamath Basin The Oregon Clim
Page 85 and 86: A change in mean precipitation rang
Page 87 and 88: Table 7.2 Impaired water bodies wit
Page 89 and 90: Table 7.3 Seasonal comparisons of p
Page 91 and 92: ammonia that is lethal to 50 percen
Page 93 and 94: Table 7.4 Estimated external phosph
Page 95 and 96: examination of juvenile suckers fro
Page 97 and 98: Evaluation of baseline hydrology in
Page 99 and 100: 2012 1931 through 2012 12.6% 0.24 5
Page 101 and 102: The overall water year trend (Table
Page 103 and 104: Figure 7.7 Sprague River trends, wa
Page 105 and 106: Figure 7.9 Sprague River trends, wa
Page 107 and 108: Figure 7.12 Williamson River trends
Page 109 and 110: Figure 7.14 UKL trends, water years
Page 111 and 112: Figure 7.17 UKL: net inflow departu
Page 113 and 114: 7.10.3.3 Competition and Predation
Page 115: By late July, surviving larval suck
Page 119 and 120: 2011) and increased adult spawning
Page 121 and 122: Based on the best available informa
Page 123 and 124: contrast, water levels began 1.5 ft
Page 125 and 126: evaporation and seepage estimated a
Page 127 and 128: prolonged low oxygen conditions if
Page 129 and 130: The April through September 4,034.6
Page 131 and 132: 8 EFFECTS OF THE ACTION ON LOST RIV
Page 133 and 134: Although the volume of Project wate
Page 135 and 136: than 1 m), and fitting one or more
Page 137 and 138: Figure 8.3. UKL elevations at the e
Page 139 and 140: Services and Reclamation will deter
Page 141 and 142: For cumulative net inflow values be
Page 143 and 144: Figure 8.8. UKL elevations at the e
Page 145 and 146: Figure 8.10. UKL elevations at the
Page 147 and 148: Figure 8.12. UKL elevations at the
Page 149 and 150: natural and man-caused changes in i
Page 151 and 152: Table 8.1 UKL end-of-month surface
Page 153 and 154: UKL. Based on best available inform
Page 155 and 156: larvae in UKL. Annual production of
Page 157 and 158: Table 8.5 UKL end-of-month elevatio
Page 159 and 160: Based on our review of the literatu
Page 161 and 162: into the Pelican Bay water quality
Page 163 and 164: We assume that UKL surface elevatio
Page 165 and 166: 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,
Page 467 and 468:
Habera, J.W., R.J. Strange, B.D. Ca
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Hemstreet, T. 2013. Electronic mail
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Jordan, M. S. 2012. Hydraulic predi
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Kostow, K. E., A. R. Marshall and S
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MacFarlane, R. B., S. Hayes, and B.
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Moyle, P. B. 2002. Inland Fishes of
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PacifiCorp Klamath Hydroelectric Pr
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Oregon Department of Environmental
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Puckridge, J. T., F. Sheldon, K. F.
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Ring, T.E. and B. Watson. 1999. Eff
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Sommer, T. R., M. L. Nobriga, W. C.
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Taylor, R. 1991. A review of local
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USFWS [U. S. Fish and Wildlife Serv
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Ward G, and Armstrong N. 2010. Asse
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Winker, K., J. H. Rappole, and M. A
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77 FR 476. National Marine Fisherie
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UKL Elevation (feet) Active Storage
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16.2 Appendix B: Elevation Flow Dat
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490
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Week of Water Year 1981 1982 1983 1
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Water Year October November Decembe
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16.3 Appendix C: Description of Res
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4. Removal of Small Dams (permanent
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Information regarding consideration
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9. Piping Ditches a. Project Descri
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. Site-Specific Restrictions Restri
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6. Protection Measures The followin
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to enter or be placed where they co
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shall be distributed throughout the
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weed free straw, silt fences) are i
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the project is located, and compris
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2. Post Construction Monitoring and
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Median Seasonal Flow (acre-feet) Me
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Median Seasonal Net Inflow (acre-fe
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16.5 Appendix E: Observed and Model
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Observed and modeled proposed actio
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Observed and modeled proposed actio
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16.6 Appendix F: Analyzing the rela
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Table 1. Paired comparison of the c
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Table 3. The difference in the mean
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