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National Marine Fisheries Service, Biological Opinion on the EPA's Proposed Approval of Certain Oregon Water Quality

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National Marine Fisheries Service, Biological Opinion on the EPA's Proposed Approval of Certain Oregon Water Quality TABLE OF CONTENTS 1. INTRODUCTION ...................................................................................................................... 2 1.1 Background ......................................................................................................................... 2 1.2 Consultation History ........................................................................................................... 2 1.3 Proposed Action .................................................................................................................. 8 1.3.1 Overview of Water Quality Standards ....................................................................... 8 1.3.2 Details of Proposed Action ........................................................................................ 9 1.4 Action Area ....................................................................................................................... 10 2. ENDANGERED SPECIES ACT .............................................................................................. 12 2.1 Analytical Approach ......................................................................................................... 13 2.2 Rangewide Status of the Species and Critical Habitat ...................................................... 14 2.2.1 Status of the Species − Fish ..................................................................................... 15 2.2.2 Status of the Species - Marine Mammals ................................................................ 53 2.2.3 Status of the Critical Habitats – Fish ....................................................................... 70 2.3 Environmental Baseline .................................................................................................... 87 2.3.1 Water Quality Environmental Baseline ................................................................... 87 2.3.2 General Environmental Baseline ............................................................................. 96 2.3.3 Marine Mammal Environmental Baseline ............................................................. 103 2.4 Effects of the Action on Species and Designated Critical Habitat ................................. 107 2.4.1 Effects of the Action on ESA-listed Fish ............................................................... 110 2.4.2 Effects of the Action on Designated Critical Habitat ............................................ 241 2.4.3 Effects of the Action on Southern Resident Killer Whales ................................... 251 2.5 Cumulative Effects.......................................................................................................... 255 2.6 Integration and Synthesis ................................................................................................ 256 2.6.1 Species ................................................................................................................... 256 2.6.2 Critical Habitat ....................................................................................................... 268 2.7 Conclusion ...................................................................................................................... 269 2.8 Reasonable and Prudent Alternative ............................................................................... 269 2.8.1. Proposed RPA ....................................................................................................... 269 2.8.2 Compliance with RPA Criteria .............................................................................. 272 2.8.3 RPA Analysis of Effects ........................................................................................ 272 2.8.4 RPA Conclusion..................................................................................................... 274 2.9 Incidental Take Statement............................................................................................... 274 2.9.1 Amount or Extent of Take ..................................................................................... 274 2.9.2 Effect of the Take................................................................................................... 278 2.9.3 Reasonable and Prudent Measures ......................................................................... 278 2.9.4 Terms and Conditions ............................................................................................ 279 2.10 Conservation Recommendations .................................................................................. 280 2.11 Reinitiation of Consultation .......................................................................................... 280 3. DATA QUALITY ACT DOCUMENTATION AND PRE-DISSEMINATION REVIEW .. 280 4. LITERATURE CITED ........................................................................................................... 282 Appendix A: ................................................................................................................................ 312 -i- 1. INTRODUCTION This Introduction section provides information relevant to the other sections of this document and is incorporated by reference into Sections 2 and 3 below. 1.1 Background The National Marine Fisheries Service (NMFS) prepared the biological opinion (opinion) and incidental take statement portions of this document in accordance with section 7(b) of the Endangered Species Act (ESA) of 1973 (16 USC 1531 et seq.), and implementing regulations at 50 CFR 402. We completed pre-dissemination review of this document using standards for utility, integrity, and objectivity in compliance with applicable guidelines issued under the Data Quality Act (section 515 of the Treasury and General Government Appropriations Act for Fiscal Year 2001, Public Law 106-554). 1.2 Consultation History The Oregon Department of Environmental Quality (DEQ) completed a triennial review of the state’s water quality standards (WQS) in January, 1996, and submitted revised standards for water temperature, dissolved oxygen and hydrogen ion concentration (pH) to the U.S. Environmental Protection Agency (EPA), Region 10, for approval under the Clean Water Act (CWA) on July 11, 1996. EPA initiated consultation on Oregon’s proposed WQS for dissolved oxygen, temperature, and pH in January 1997. On September 18, 1998, EPA submitted a biological assessment (BE) (EPA 1998) for EPA’s proposed approval of Oregon’s revised WQS. We issued an opinion on EPA’s proposed action on July 7, 1999 (NMFS 1999a). The opinion concluded that EPA’s proposed approval of Oregon’s WQS was not likely to jeopardize the continued existence of the listed, proposed, and candidate species named in the BA, or result in the destruction or adverse modification of their critical habitat. To address issues raised in the ESA consultation on its 1999 approval action, EPA proposed an intergovernmental project to develop guidance for water temperature criteria for use in the Pacific Northwest. We also required completion of this project in our July, 1999 opinion. The goal for this project was to develop guidance that: • Meets the biological requirements of native salmonid species for survival and recovery pursuant to ESA • Provides for the restoration and maintenance of surface water temperature to support and protect native salmonids pursuant to the CWA • Meets the salmon rebuilding needs of Federal trust responsibilities with treaty tribes • Recognizes the natural temperature potential and limitations of water bodies • Can be effectively incorporated by states and tribes in water quality standards programs • Will be used by states and tribes to revise their temperature standards, if necessary -2- • Will be used by EPA, NMFS and U.S. Fish and Wildlife Service to evaluate state and tribal standard revisions1 We endorsed the final guidance document (April 23, 3002, letter from Robert Lohn, NMFS, to John Iani, EPA Region 10), and consider the Temperature Guidance to include the best scientific information available at the time on the thermal requirements of salmon and steelhead and on how to construct state or tribal water quality criteria for temperature. The EPA’s CWA approval document and NMFS’ 1999 biological opinion were challenged by Northwest Environmental Advocates (NWEA), which filed a lawsuit in April 2001, challenging the Federal agencies’ decision regarding Oregon’s WQS. On March 31, 2003, the U.S. District Court for Oregon invalidated EPA’s approval of Oregon’s revised standards, and directed EPA to promulgate the following Federal WQS for Oregon waters: • numeric criteria for the protection of salmonid rearing and bull trout rearing and spawning, accompanied by specific time and place use designations; • a numeric temperature criterion for the lower Willamette River; • a water quality criterion for intergravel dissolved oxygen (IGDO) for the protection of salmonid spawning; and • a plan for implementing the antidegradation policy adopted by Oregon. The March 31, 2003 court decision also invalidated the opinion issued by NMFS in 1999 on EPA’s proposed approval of new and revised Oregon WQS. The court ordered NMFS to withdraw its opinion and reinitiate consultation with the EPA under the ESA. In accordance a stipulated schedule, the Court ordered NMFS to sign and transmit to EPA a final opinion within 53 days of receipt of a BE. On December 10, 2003, Oregon revised its WQS to address the issues raised in the March, 31 2003 court order and subsequently submitted the WQS to EPA for approval.
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