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US Fish and Wildlife Service Biological Opinion

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US Fish and Wildlife Service Biological Opinion U.S. Fish and Wildlife Service Biological Opinion for Bureau of Reclamation Operations and Maintenance in the Snake River Basin Above Brownlee Reservoir U.S. Fish and Wildlife Service Snake River Fish and Wildlife Office Boise, Idaho March 2005 TABLE OF CONTENTS Chapter 1 Introduction............................................................................................................1 I. Introduction..............................................................................................................1 II. Background..............................................................................................................2 A. Project Authorizations....................................................................................2 B. Hydrologic Seasons and Operations ...............................................................5 C. Snake River Basin Adjudication.....................................................................5 D. Flow Augmentation for Salmon......................................................................6 III. Consultation History................................................................................................9 IV. Concurrence ...........................................................................................................12 V. Climate...................................................................................................................13 VI. Reinitiation Notice.................................................................................................14 VII. Consultation with American Indian Tribes............................................................14 VIII. Literature Cited ......................................................................................................15 Chapter 2 Description of the Proposed Action....................................................................17 I. Operations on the South Fork of the Snake River .................................................17 A. Jackson Lake Dam and Lake ........................................................................17 B. Palisades Dam and Reservoir........................................................................18 II. Operations in the Henrys Fork System ..................................................................20 A. Grassy Lake Dam and Lake..........................................................................20 B. Island Park Dam and Reservoir ....................................................................21 III. Operations on Willow Creek.................................................................................22 IV. Operations on the Mainstem Snake River .............................................................23 A. American Falls Dam and Reservoir..............................................................24 B. Falls Irrigation Pumping Plant......................................................................26 C. Minidoka Dam and Lake Walcott.................................................................26 D. Milner Dam and Pool....................................................................................28 E. Dead Ox, Owyhee Ditch, Ontario/Nyssa, and Gem Pumping Plants ...........30 V. Operations on the Little Wood River.....................................................................32 VI. Operations on the Owyhee River...........................................................................32 VII. Operations in the Boise River System ...................................................................34 A. Anderson Ranch Dam and Reservoir............................................................34 B. Arrowrock Dam and Reservoir.....................................................................36 C. Lucky Peak Dam and Reservoir ...................................................................38 D. Deer Flat Dams and Lake Lowell .................................................................39 March 2005 U.S. Fish and Wildlife Service i Table of Contents VIII. Operations in the Malheur River System...............................................................40 A. Warm Springs Dam and Reservoir ...............................................................40 B. Agency Valley Dam and Beulah Reservoir..................................................41 C. Bully Creek Dam and Reservoir...................................................................41 IX. Operations in the Payette River System.................................................................42 A. Deadwood Dam and Reservoir .....................................................................42 B. Cascade Dam and Lake Cascade ..................................................................44 X. Operations on Mann Creek ....................................................................................45 XI. Operations on the Burnt River ...............................................................................46 XII. Operations in the Powder River System ................................................................47 A. Mason Dam and Phillips Lake......................................................................47 B. Thief Valley Dam and Reservoir ..................................................................47 XIII. Routine Maintenance .............................................................................................48 XIV. Literature Cited ......................................................................................................48 Chapter 3 Environmental Conditions in the Action Area .................................................51 I. Geographic Setting and Hydrology .......................................................................51 II. Climate...................................................................................................................53 III. Water Use and Quantity.........................................................................................53 A. Hydroelectric Facilities.................................................................................53 B. Irrigation Facilities........................................................................................55 1. Surface Water.......................................................................................55 2. Groundwater ........................................................................................57 3. Other Factors Affecting Water Quality................................................58 IV. Water Quality.........................................................................................................58 A. Surface Water................................................................................................58 1. Point Source Discharges ......................................................................59 2. Nonpoint Source Discharges................................................................60 3. Other Sources.......................................................................................61 B. Groundwater .................................................................................................61 C. Water Quality Standards and Total Maximum Daily Load Limits...............62 D. Fish Consumption Advisories.......................................................................63 V. Introduced Species.................................................................................................63 VI. Literature Cited......................................................................................................64 Chapter 4 Bald Eagle.............................................................................................................69 I. Status of the Species ..............................................................................................69 A. Regulatory Status..........................................................................................69 B. Description of the Species ............................................................................69 ii U.S. Fish and Wildlife Service March 2005 Table of Contents C. Status and Distribution..................................................................................69 D. Life History...................................................................................................70 1. Nesting Habitat....................................................................................70 2. Wintering Habitat.................................................................................70 E. Population Dynamics....................................................................................71 F. Conservation Needs......................................................................................71 II. Environmental Baseline.........................................................................................72 A. Status of the Species in the Action Area.......................................................72 1. Snake River Basin above Milner Dam in Wyoming and Idaho...........72 2. Snake River from Milner Dam to Brownlee Reservoir .......................73 3. Snake River from Brownlee Reservoir to the Columbia River and Columbia River to its Mouth ...............................................................74 4. Little Wood River Reservoir................................................................74 5. Boise and Payette River Basins ...........................................................74 6. Owyhee River Basin ............................................................................77
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