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Biological Evaluation of the NPDES General Permit for Hydroelectric Facilities Within the State of Idaho Permit Number IDG360000

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Biological Evaluation of the NPDES General Permit for Hydroelectric Facilities Within the State of Idaho Permit Number IDG360000 Biological Evaluation of the NPDES General Permit for Hydroelectric Facilities Within the State of Idaho Permit Number IDG360000 Prepared for: US Fish and Wildlife Service and National Oceanic and Atmospheric Administration – Fisheries Prepared by: US Environmental Protection Agency, Region 10 Office of Water 1200 Sixth Avenue, Suite 900 Seattle, WA 98101 February 2018 Executive Summary The U.S. Environmental Protection Agency (USEPA) conducted a biological evaluation to identify potential impacts to federally listed Endangered or Threatened species that could result from the issuance of the National Pollutant Discharge Elimination System (NPDES) General Permit to hydroelectric facilities operating in the State of Idaho. The proposed Hydroelectric Facility General Permit (General Permit) authorizes the following types of discharges from hydroelectric facilities into waters of the State of Idaho: equipment cooling water, equipment and floor drain water, equipment backwash strainer water, and specific maintenance waters. The General Permit places effluent limits on the discharges for oil, grease, and pH, monitoring requirements for oil, grease and temperature, and requirements for best management practices. The General Permit does not regulate the river flow through the turbines or over the dam. The Threatened and Endangered Species of concern identified for this action are: Endangered Species: Snake River Sockeye salmon (Oncorhynchus nerka) Kootenai River White Sturgeon (Acipenser transmontanus) Banbury Springs Lanx (Lanx sp.) Bruneau Hot Spring Snail (Pyrgulopsis brungeuenis) Snake River Physa Snail (Physa natricina) Ute Ladies’ Tresses Orchid ((Spiranthes divulvialis) Water Howellia (Howellia aquatilis) Threatened Species: Snake River Spring/summer Chinook salmon (O. tshawytscha) Snake River Fall Chinook salmon (O. tshawytscha) Snake River Steelhead (O. mykiss) Bull trout (Salvelinus confluentus) Bliss Rapids Snail (Taylorconcha serpenticola) The EPA has determined that issuance of the General Permit for hydroelectric facilities is not likely to adversely affect Snake River Sockeye salmon, Snake River Spring/Summer and Fall Chinook salmon, Snake River Steelhead, and Bull trout, Banbury Springs Lanx, , Snake River Physa Snail, Bliss Rapids Snail and Ute Ladies’ Tresses Orchid. The EPA has determined that issuance of the General Permit will have no effect on Kootenai River White sturgeon, Bruneau Hot Spring Snail, and Water Howellia. The EPA has also determined that issuance of the General Permit is not likely to adversely affect the Critical Habitat designated for Bull Trout, Snake River Chinook, Snake River Steelhead, and Snake River Sockeye. 2 Biological Evaluation of the General Permit for Hydro-electric in the State of Idaho Table of Contents Table of Contents .................................................................................................................................. 3 1 Description of the Proposed Action ...................................................................................................... 8 Description of Hydroelectric Generating Facilities ...................................................................... 8 Discharges from Hydro-Electric Facilities.................................................................................... 9 Scope of General Permit ............................................................................................................. 12 1.3.1 Eligibility Requirements ..................................................................................................... 12 1.3.2 Hydro-electric Facilities Ineligible for Coverage ............................................................... 12 1.3.3 Authorized Discharges ........................................................................................................ 12 1.3.4 Effluent Limits and Monitoring Requirements ................................................................... 13 1.3.5 Operating Requirements ..................................................................................................... 15 2 Threatened and Endangered Species ................................................................................................... 18 Species Status, Life History, and Distribution for Species of Concern ...................................... 21 2.1.1 Snake River Fall Chinook Salmon ...................................................................................... 21 2.1.2 Snake River Spring and Summer Chinook Salmon ............................................................ 22 2.1.3 Snake River Sockeye Salmon ............................................................................................. 23 2.1.4 Snake River Steelhead ........................................................................................................ 24 2.1.5 Bull Trout ............................................................................................................................ 26 2.1.6 Kootenai River White Sturgeon .......................................................................................... 28 2.1.7 Banbury Springs Lanx ........................................................................................................ 29 2.1.8 Bliss Rapids Snail ............................................................................................................... 30 2.1.9 Bruneau Hot Spring Snail ................................................................................................... 31 2.1.10 Snake River Physa Snail ..................................................................................................... 32 2.1.11 Ute Ladies’ Tresses Orchid ................................................................................................. 32 2.1.12 Water Howellia ................................................................................................................... 33 3 Environmental Baseline ...................................................................................................................... 35 Description of Action Area ......................................................................................................... 35 Current Status of the Environment .............................................................................................. 35 4 Exposure Assessment .......................................................................................................................... 39 Plants ........................................................................................................................................... 39 Fish .............................................................................................................................................. 39 Invertebrates ................................................................................................................................ 39 5 Analysis of Effects .............................................................................................................................. 40 Methodology ............................................................................................................................... 41 Impacts of Pollutants of Concern (pH, Temperature, Oil and Grease) ....................................... 41 _Toc505176913 3 Biological Evaluation of the General Permit for Hydro-electric in the State of Idaho Determining Receiving Water Concentrations as a Result of Permit Limits .............................. 43 Determination of Effect on Species of Concern ......................................................................... 48 5.4.1 Fish ...................................................................................................................................... 48 5.4.2 Invertebrates ........................................................................................................................ 49 5.4.3 Plants ................................................................................................................................... 49 Clean Water Act 316(b) Requirements ....................................................................................... 50 Determination of Effect on Critical Habitat ................................................................................ 50 Summary of Effects Determinations ........................................................................................... 52 6 Cumulative Effects and Interdependent/Interrelated Actions ............................................................. 54 7 Essential Fish Habitat Analysis for Idaho’s NPDES Permit for Hydroelectric Dams ........................ 55 Essential Fish Habitat Background ............................................................................................. 55 Description of the Action/Action Area ....................................................................................... 55 Potential Adverse Effects of Proposed Project on Salmon EFH ................................................. 55 EFH Conservation Measures ...................................................................................................... 56 Conclusions ................................................................................................................................. 56 8 References ........................................................................................................................................... 57 Table
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