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Endangered Species Act Biological Opinion and Magnuson-Stevens

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Endangered Species Act Biological Opinion and Magnuson-Stevens UNITED STATES DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration NA TIO NAL MARINE FISHERIES SERVICE 1201 NE Lloyd Boulevard. SUite 1100 PORT LAND, OREGON 97232·1274 January 11 , 2013 Lorri Lee Pacific Northwest Regional Director U .S. Bureau ofReclamation 1160 North Curtis Road, Suite 100 Boise, Idaho 83706-1234 Re: Endangered Species Act Section 7(a)(2) Biological Opinion and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat Consultation for the U.S. Bureau of Reclamation's Odessa Subarea Modified Partial Groundwater Replacement Project. (NWR-2012-9371) Dear Ms. Lee: Enclosed is the Endangered Species Act (ESA) Biological Opinion and Magnuson-Stevens Fishery Conservation and Management Act (MSA) Essential Fish Habitat (EFH) Consultation prepared by National Marine Fisheries Service (NMFS) regarding the U.S. Bureau of Reclamation's (Reclamation) Odessa Subarea Modified Partial Groundwater Replacement Project on the Colwnbia River in Adams, Lincoln, Franklin and Grant Counties, Washington. NMFS received a final biological assessment (BA) from Reclamation on November 6, 2012. Reclamation's BA determined that Columbia River chum salmon were likely to be adversely affected by the proposed action, 12 other species ofESA listed salmon and steelhead would not likely be adversely affected by the proposed action, and that Pacific eulachon, green sturgeon, and southern resident killer whales would not likely be adversely affected by the proposed action. NMFS disagreed with Reclamation's "Not Likely to Adversely Affect" detenninations for 12 species ofsalmon and steelhead. NMFS 's Biological Opinion (Section 2 ofthe enclosed document) analyzes the effects ofthe proposed Federal action on all 13 ESA-listed salmon and steelhead species in the Columbia River Basin: Upper Columbia River spring Chinook salmon, Upper Columbia River steelhead, Mid-Columbia River steelhead, Snake River spring/swnmer Chinook salmon, Snake River fall Chinook salmon, Snake River sockeye, Snake River steelhead, Columbia River chum salmon, Lower Columbia River Chinook salmon, Lower Columbia River steelhead, Lower Columbia River coho salmon, Upper Willamette River Chinook salmon, and Upper Willamette River steelhead in accordance with Section 7 ofthe Endangered Species Act (ESA) of 1973 as amended (16 USC 1531 et seq.). NMFS concludes that the proposed action is not likely to jeopardize the continued existence ofthese 13 species, or destroy or adversely modify their designated critical habitat. 2 Section 3 of the enclosed document is a consultation regarding EFH under the MSA, as amended by the Sustainable Fisheries Act of 1996 (Public Law 104-267). NMFS finds that the proposed action could adversely affect Chinook salmon EFH in the Hanford Reach of the Columbia River and recommends that Reclamation curtail diversions for Odessa project when flows at Priest Rapids Dam fall below 40,000 cfs. Pursuant to MSA (§ 305(b)(4)(B)) and 50 CFR 6000.920(j), Federal agencies are required to provide a written response to NMFS' EFH conservation recommendations within 30 days of receipt ofthose recommendations. NMFS would also like to note issues, which were raised through our consultations with several affected tribes. First, there are concerns about the number and magnitude of Columbia River Basin water withdrawal proposals being raised through state processes, and what cumulative effects these withdrawal might have on the survival and behavior of migrating salmon if they are implemented. The tribes have asked for, and NMFS supports, further dialogue with Reclamation, NMFS, and other regional stakeholders regarding this issue. Second, the tribes, and NMFS, recognize that substantial efforts are underway to better understand how juvenile salmon and steelhead are using habitat within the Columbia River estuary, and how that use and timing relates to survival throughout their life cycle. The new information obtained from these studies should substantially improve our understanding of how a variety of factors affect the conservation value ofthis habitat and the upstream migratory corridor. NMFS encourages Reclamation to keep abreast of the information coming out of these studies and integrate these findings into their processes for considering long-term water management operations. Comments or questions regarding this Biological Opinion and MSA consultation should be directed to Rich Domingue at 503.231.6858 or([email protected]) or Ritchie Graves, FCRPS Branch Chief, at 503.231.6891 ([email protected]). ,;::::~:-41/? -FiSV'l--"' William W. Stelle, Jr Regional Administrator cc: Wendy Christenson (USBR) Gerald Kelso (USBR) Endangered Species Act (ESA) Section 7(a)(2) Biological Opinion, Section 7(a)(2) "Not Likely to Adversely Affect" Determination, Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat (EFH) Consultation Odessa Subarea Partial Groundwater Replacement Project NMFS Consultation Number: NWR-2012-9371 Action Agency: U.S. Bureau ofReclamation Affected Species and Determinations: ESA-Listed Species Status Is Action Is Action Is Action Likely To Likely to Likely To Destroy or Adversely Jeopardize Adversely Modify Affect the Species? Critical Habitat? Species or Critical Habitat? Snake River steelhead Threatened Yes No No (Oncorhynchus mykiss) Upper Columbia River Threatened Yes No No steelhead ( 0. mykiss) Middle Columbia River Threatened Yes No No steelhead (0. mykiss) Lower Columbia River Threatened Yes No No steelhead ( 0. mykiss) Upper Willamette River Threatened Yes No No steelhead ( 0. mykiss) Snake River fall Chinook Threatened Yes No No (0. tshaw)!.tscha) Snake River Threatened Yes No No spring/summer Chinook (0. tshawvtscha) Upper Columbia River Endangered Yes No No Chinook (0. tshawytscha) Lower Columbia River Threatened Yes No No (0. tshawvtscha) Upper Willamette River Threatened Yes No No (0. tshawytscha) Snake River Sockeye (0. Endangered Yes No No nerka) Lower Columbia River Threatened Yes No No coho ( 0. kisutch) Columbia River chum Threatened Yes No No (0. keta) Southern green sturgeon Threatened No (Acipense meiorostris) Eulochon (Thaleichthys Threatened No pacificus) Southern resident killer Threatened No whale (Orcinus orca) Fishery Management Plan Does Action Have an Adverse Are EFH Conservation That Describes EFH in the Effect on EFH? Recommendations Provided? Project Area Pacific Coast Salmon Yes Yes Issued By: Date: I I TABLE OF CONTENTS TABLE OF CONTENTS ............................................................................................................... 3 TABLE OF FIGURES ................................................................................................................... 6 TABLE OF TABLES ..................................................................................................................... 8 TERMS AND ABBREVIATIONS ............................................................................................. 9 1. INTRODUCTION ................................................................................................................. 11 1.1 BACKGROUND .......................................................................................................................... 11 1.2 CONSULTATION HISTORY ........................................................................................................... 11 1.3 PROPOSED ACTION ................................................................................................................... 13 1.3.1 Diversions from the Columbia River ............................................................................ 15 1.3.1.1 Other Water Storage and Conveyance Operations .............................................. 18 1.3.2 Water Accounting and Monitoring .............................................................................. 18 1.3.3 Environmental Commitments ...................................................................................... 18 1.4 ACTION AREA .......................................................................................................................... 18 2. ENDANGERED SPECIES ACT: BIOLOGICAL OPINION ........................................................... 20 AND INCIDENTAL TAKE STATEMENT ...................................................................................... 20 2.1 APPROACH TO THE ANALYSIS ................................................................................................ 20 2.2 RANGEWIDE STATUS OF THE SPECIES AND CRITICAL HABITAT ...................................................... 21 2.2.1 Status of Listed Species ............................................................................................. 21 2.2.1.1 Salmonids in the Interior Columbia (IC) Recovery Domain ................................. 24 2.2.1.2 Salmonids in the Willamette/Lower Columbia Recovery (WLC) Domain ............ 43 2.2.1.3 Non‐Salmonids ..................................................................................................... 63 2.2.2 Status of Critical Habitat ........................................................................................... 71 2.2.2.1 Salmon and Steelhead ......................................................................................... 71 2.2.2.2 Non‐Salmonid Species .......................................................................................... 75 2.3 ENVIRONMENTAL BASELINE .......................................................................................................
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