APPLICANT-PREPARED ESSENTIAL FISH HABITAT ASSESSMENT DON PEDRO PROJECT FERC NO. 2299 Prepared for: Turlock Irrigation District – Turlock, California Modesto Irrigation District – Modesto, California Prepared by: HDR Engineering, Inc. September 2017 This Page Intentionally Left Blank. TABLE OF CONTENTS Section No. Description Page No. PREFACE ................................................................................................................................. XIII 1.0 INTRODUCTION.......................................................................................................... 1-1 1.1 Essential Fish Habitat Regulatory Framework .................................................... 1-1 1.2 EFH Action Area ................................................................................................. 1-1 1.3 Public Review and Consultation during Relicensing........................................... 1-2 1.3.1 Notice of Intent and Pre-Application Document ..................................... 1-2 1.3.2 Scoping and Study Plan Development ..................................................... 1-4 1.3.3 Pre-Filing Consultation Workshop Process ............................................. 1-5 1.3.4 Initial and Updated Study Reports ........................................................... 1-6 1.3.5 Draft License Application ........................................................................ 1-6 1.3.6 Post-Filing Consultation and Alternatives Analysis ................................ 1-7 2.0 PROJECT DESCRIPTION .......................................................................................... 2-1 2.1 Project Boundary ................................................................................................. 2-1 2.2 Existing Project Facilities .................................................................................... 2-1 2.2.1 Don Pedro Dam........................................................................................ 2-1 2.2.2 Don Pedro Reservoir ................................................................................ 2-1 2.2.3 Don Pedro Spillway ................................................................................. 2-3 2.2.4 Outlet Works ............................................................................................ 2-3 2.2.5 Power Intake and Tunnel ......................................................................... 2-3 2.2.6 Powerhouse, Turbines, and Generators ................................................... 2-4 2.2.7 Tailwater .................................................................................................. 2-4 2.2.8 Switchyard ............................................................................................... 2-4 2.2.9 Gasburg Creek Dike ................................................................................. 2-5 2.2.10 Dikes A, B, and C .................................................................................... 2-5 2.2.11 Station Service ......................................................................................... 2-5 2.2.12 Recreation Facilities................................................................................. 2-5 2.2.12.1 Fleming Meadows Recreation Area ....................................... 2-5 2.2.12.2 Blue Oaks Recreation Area .................................................... 2-5 2.2.12.3 Moccasin Point Recreation Area ........................................... 2-6 2.3 Existing Project Operations ................................................................................. 2-6 2.3.1 Primary Purposes of the Don Pedro Project ............................................ 2-6 2.3.2 Overview of Don Pedro Project Operations ............................................ 2-6 2.4 Existing Environmental Measures ....................................................................... 2-8 2.4.1 Existing FERC-Mandated Flow Regime for the Lower Tuolumne River2-8 2.4.2 District-Funded Existing Non-Flow Measures in the Lower Tuolumne River ......................................................................................................... 2-8 Fall-Run Chinook Salmon i EFH Assessment September 2017 Don Pedro Hydroelectric Project Table of Contents 3.0 PROPOSED ACTION AND MEASURES .................................................................. 3-1 3.1 Proposed Action ................................................................................................... 3-1 3.1.1 Proposed Aquatic Resource Measures ..................................................... 3-2 3.2 Interrelated and Interdependent Actions .............................................................. 3-5 4.0 EXISTING CONDITIONS IN THE ACTION AREA ............................................... 4-1 4.1 Delineation of EFH Action Area ......................................................................... 4-1 4.2 Overview of the EFH Action Area ...................................................................... 4-1 4.2.1 Lower Tuolumne River ............................................................................ 4-1 4.2.2 Lower San Joaquin River ......................................................................... 4-2 4.2.3 Sacramento-San Joaquin Delta ................................................................ 4-3 4.3 Central Valley Fall-Run Chinook Salmon ........................................................... 4-3 4.3.1 Fall-Run Chinook Studies in the Lower Tuolumne River ....................... 4-4 4.3.1.1 Spawning Gravel in the Lower Tuolumne River (W&AR-04) 4- 9 4.3.1.2 Salmonid Population Information Integration and Synthesis (W&AR-05) ......................................................................... 4-10 4.3.1.3 Chinook Salmon Population Model Study (W&AR-06) ..... 4-10 4.3.1.4 Predation (W&AR-07) ......................................................... 4-10 4.3.1.5 Salmonid Redd Mapping (W&AR-08) ................................ 4-11 4.3.1.6 Chinook Salmon Otolith Study (W&AR-11) ...................... 4-11 4.3.1.7 Lower Tuolumne River Floodplain Hydraulic Assessment (W&AR-21) ......................................................................... 4-11 4.3.1.8 One-Dimensional (1-D) PHABSIM model (Stillwater Sciences 2013) .................................................................................... 4-12 4.3.1.9 Tuolumne River Flow and Water Temperature Model: Without Dams Assessment (Jayasundara et al. 2017) ....................... 4-12 4.3.2 Tuolumne River Fall-Run Chinook Salmon .......................................... 4-12 4.3.2.1 Adult Immigration ............................................................... 4-12 4.3.2.2 Spawning and Incubation ..................................................... 4-15 4.3.2.3 Juvenile Rearing, Smoltification, and Outmigration ........... 4-17 4.3.3 Threats and Stressors to Fall-Run Chinook Salmon in the EFH Action Area ........................................................................................................ 4-20 4.3.4 Conservation Initiatives ......................................................................... 4-24 4.4 Habitat Conditions in the Action Area ............................................................... 4-26 4.4.1 Overview of Habitat Conditions in the Lower Tuolumne River ........... 4-26 4.4.1.1 Hydrology in the in the Lower Tuolumne River ................. 4-28 4.4.1.2 Temperature and Water Quality in the Lower Tuolumne River .............................................................................................. 4-30 4.4.1.2.1 Temperature ......................................................................... 4-30 Fall-Run Chinook Salmon ii EFH Assessment September 2017 Don Pedro Hydroelectric Project Table of Contents 4.4.1.2.2 Water Quality ....................................................................... 4-35 4.4.1.3 Fall-Run Chinook Habitat in the Lower Tuolumne River ... 4-40 4.4.1.3.1 Spawning and Incubation ..................................................... 4-40 4.4.1.3.2 Juvenile Rearing, Smoltification, and Outmigration ........... 4-42 4.4.2 Habitat Conditions in the lower San Joaquin River and Delta .............. 4-44 4.4.2.1 Lower San Joaquin River ..................................................... 4-44 4.4.2.1.1 Hydrology and Geomorphology of the Lower San Joaquin River ..................................................................................... 4-45 4.4.2.1.2 Temperature in the Lower San Joaquin River ..................... 4-46 4.4.2.1.3 Water Quality in the in the Lower San Joaquin River ......... 4-46 4.4.2.2 Sacramento-San Joaquin Delta ............................................ 4-47 5.0 EFFECTS OF PROPOSED ACTION ......................................................................... 5-1 5.1 Interrelated and Interdependent Actions .............................................................. 5-1 5.2 Direct and Indirect Effects of the Proposed Action ............................................. 5-1 5.2.1 Effects of Proposed Aquatic Resources Measures................................... 5-2 5.2.1.1 Improve Spawning Gravel Quantity and Quality .................. 5-2 5.2.1.1.1 Augment Current Gravel Quantities through a Coarse Sediment Management Program ............................................................ 5-2 5.2.1.1.2 Gravel Mobilization Flows of 6,000 to 7,000 cfs .................. 5-3 5.2.1.1.3 Gravel Cleaning ..................................................................... 5-4 5.2.1.2