APPLICANT-PREPARED DRAFT BIOLOGICAL ASSESSMENT CALIFORNIA CENTRAL VALLEY STEELHEAD (Oncorhynchus mykiss) DISTINCT POPULATION SEGMENT DON PEDRO HYDROELECTRIC 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. 1.0 INTRODUCTION.......................................................................................................... 1-1 1.1 Proposed Action and FERC Authority ................................................................ 1-1 1.1.1 Regulatory Framework ............................................................................ 1-2 1.2 Project Background .............................................................................................. 1-2 1.2.1 Project Boundary and Facilities ............................................................... 1-3 1.3 Public Review and Consultation during Relicensing ........................................... 1-5 1.3.1 Notice of Intent and Pre-Application Document ..................................... 1-5 1.3.2 Scoping and Study Plan Development ..................................................... 1-5 1.3.3 Pre-Filing Consultation Workshop Process ............................................. 1-7 1.3.4 Initial and Updated Study Reports ........................................................... 1-8 1.3.5 Draft License Application ........................................................................ 1-8 1.3.6 Post-Filing Consultation and Alternatives Analysis ................................ 1-8 2.0 DESCRIPTION OF THE PROPOSED ACTION ...................................................... 2-1 2.1 Proposed Action ................................................................................................... 2-1 2.1.1 Improve Spawning Gravel Quantity and Quality .................................... 2-2 2.1.1.1 Augment Current Gravel Quantities through a Coarse Sediment Management Program ............................................................ 2-2 2.1.1.2 Gravel Mobilization Flows of 6,000 to 7,000 cfs .................. 2-3 2.1.1.3 Gravel Cleaning ..................................................................... 2-4 2.1.2 Improve Instream Habitat Complexity .................................................... 2-4 2.1.3 Contribute to CDBW’s Efforts to Remove Water Hyacinth ................... 2-5 2.1.4 Fall-Run Chinook Spawning Improvement Superimposition Reduction Program .................................................................................................... 2-5 2.1.5 Predator Control and Suppression Plan ................................................... 2-5 2.1.5.1 Construct a Fish Counting and Barrier Weir ......................... 2-6 2.1.5.2 Predator Suppression and Removal ....................................... 2-8 2.1.6 Fall-Run Chinook Salmon Restoration Hatchery Program ..................... 2-9 2.1.7 Infiltration Galleries 1 and 2 .................................................................... 2-9 2.1.8 Flow-Related Measures for Fish and Aquatic Resources ...................... 2-10 2.1.8.1 Early Summer O. mykiss Fry Rearing (June 1–June 30) ..... 2-12 2.1.8.2 Late Summer O. mykiss Juvenile Rearing (July 1–October 15) .............................................................................................. 2-13 2.1.8.3 Fall-Run Chinook Spawning Flows (October 16– December 31) ....................................................................... 2-13 2.1.8.4 Fall-Run Chinook Fry Rearing (January 1– February 28/29) .................................................................... 2-13 2.1.8.5 Fall-run Chinook Juvenile Rearing (March 1–April 15) ..... 2-13 California CV Steelhead Page i Biological Assessment September 2017 Don Pedro Hydroelectric Project Table of Contents 2.1.8.6 Fall-run Chinook Outmigration Base Flows (April 16– May 15) ................................................................................ 2-14 2.1.8.7 Outmigration Base Flows (May 16–May 31) ...................... 2-14 2.1.8.8 Outmigration Pulse Flows (April 16–May 31) .................... 2-14 2.1.8.9 Flow Hydrograph Shaping ................................................... 2-14 2.1.9 Flows to Enhance Recreational Boating ................................................ 2-15 2.2 Interrelated and Interdependent Actions ............................................................ 2-15 2.3 Action Area ........................................................................................................ 2-16 3.0 CALIFORNIA CENTRAL VALLEY STEELHEAD DPS........................................ 3-1 3.1 ESA Listing of the CCV Steelhead ...................................................................... 3-1 3.1.1 Status of the CCV Steelhead DPS ........................................................... 3-2 3.1.2 Life History and Ecology ......................................................................... 3-3 3.1.2.1 Adult Upstream Migration and Spawning ............................. 3-3 3.1.2.2 Egg Incubation and Fry Emergence ....................................... 3-4 3.1.2.3 Freshwater Rearing and Smolt Outmigration ........................ 3-5 3.1.2.4 Ocean Phase ........................................................................... 3-5 3.1.2.5 Anadromy Versus Residency in Oncorhynchus mykiss ......... 3-6 3.1.3 Historical and Current Distribution of CCV Steelhead ........................... 3-6 3.1.4 Designated Critical Habitat in the San Joaquin River Basin ................... 3-7 3.1.5 Stressors and Limiting Factors................................................................. 3-8 3.1.6 Recovery Criteria ................................................................................... 3-14 3.1.7 Conservation Initiatives ......................................................................... 3-14 3.1.7.1 Existing FERC-Mandated Flow Regime for the Lower Tuolumne River ................................................................... 3-15 3.1.7.2 District-Funded Existing Non-Flow Measures in the Lower Tuolumne River ................................................................... 3-17 4.0 ENVIRONMENTAL BASELINE IN THE ACTION AREA .................................... 4-1 4.1 Studies Related to O. mykiss in the Action Area ................................................. 4-1 4.1.1 Spawning Gravel in the Lower Tuolumne River (W&AR-04) ............... 4-1 4.1.2 Salmonid Population Information Integration and Synthesis (W&AR-05) ............................................................................................. 4-2 4.1.3 Salmonid Redd Mapping (W&AR-08) .................................................... 4-2 4.1.4 Oncorhynchus mykiss Population Study (W&AR-10) ............................ 4-2 4.1.5 Oncorhynchus mykiss Habitat Survey (W&AR-12) ................................ 4-3 4.1.6 Temperature Criteria Assessment (W&AR-14)....................................... 4-3 4.1.7 Oncorhynchus mykiss Scale Collection and Age Determination (W&AR-20) ............................................................................................. 4-3 4.1.8 Lower Tuolumne River Floodplain Hydraulic Assessment (W&AR-21) ............................................................................................. 4-4 California CV Steelhead Page ii Biological Assessment September 2017 Don Pedro Hydroelectric Project Table of Contents 4.1.9 One-Dimensional (1-D) PHABSIM model (Stillwater Sciences 2013) .. 4-4 4.1.10 Tuolumne River Flow and Water Temperature Model: Without Dams Assessment (Jayasundara et al. 2017) ...................................................... 4-5 4.2 Fish Assemblage in the Action Area ................................................................... 4-5 4.3 Existing Physical Habitat Conditions in the Action Area .................................... 4-7 4.4 Hydrology in the Action Area.............................................................................. 4-9 4.4.1 Unimpaired Flow ................................................................................... 4-10 4.4.2 Flood Hydrology .................................................................................... 4-11 4.4.3 Drought Hydrology ................................................................................ 4-11 4.5 Temperature and Water Quality in the Action Area .......................................... 4-11 4.5.1 Temperature ........................................................................................... 4-11 4.5.2 Water Quality ......................................................................................... 4-15 4.6 Status of the O. mykiss Population in the Action Area ...................................... 4-17 4.6.1 Anadromy Versus Residency ................................................................. 4-17 4.6.2 Absence of Anadromous O. mykiss in the Lower Tuolumne River ...... 4-18 4.6.3 O. mykiss Spawning in the Action Area ................................................ 4-19 4.6.4 O. mykiss Rearing in the Action Area .................................................... 4-22 4.6.5 Adult O. mykiss Upstream Migration .................................................... 4-24 4.6.6 O. mykiss Growth and Productivity ....................................................... 4-25 4.6.7 Effects of Existing Flow Regime ..........................................................