Initial Study of the Long-Term Operation of the State Water Project State Clearinghouse No. 2019049121 State of California Department of Water Resources November 22, 2019 Initial Study of the Long-Term Operation of the State Water Project State Clearinghouse No. 2019049121 Lead Agency: California Department of Water Resources Contact: Dean Messer, Division of Environmental Services, Regulatory Compliance Branch 916/376-9844 Responsible Agency: California Department of Fish and Wildlife November 22, 2019 TABLE OF CONTENTS 1 INTRODUCTION .................................................................................................................... 1-1 1.1 Background ...................................................................................................................... 1-1 1.2 Project Objectives ............................................................................................................ 1-2 1.2.1 Required Permits and Approvals ......................................................................... 1-2 1.2.2 Document Organization ....................................................................................... 1-2 1.3 Summary of Findings........................................................................................................ 1-3 2 PROJECT DESCRIPTION .......................................................................................................... 2-1 2.1 Introduction ..................................................................................................................... 2-1 2.1.1 Project Objectives ................................................................................................ 2-1 2.1.2 Project Location ................................................................................................... 2-1 2.1.3 Description of Existing SWP Facilities .................................................................. 2-4 2.1.3.1 Harvey O. Banks Pumping Plant ............................................................ 2-4 2.1.3.2 John E. Skinner Delta Fish Protective Facility ....................................... 2-4 2.1.3.3 Clifton Court Forebay ............................................................................ 2-4 2.1.3.4 Barker Slough Pumping Plant ............................................................... 2-5 2.1.3.5 Suisun Marsh Operations ...................................................................... 2-5 2.1.3.6 South Delta Temporary Barrier Project ................................................ 2-7 2.1.3.7 Head of Old River Barrier ...................................................................... 2-7 2.1.3.8 San Luis Reservoir ................................................................................. 2-8 2.1.4 Description of Existing SWP Water Service Contracts ......................................... 2-8 2.1.5 SWP Allocation and Forecasting ........................................................................ 2-11 2.1.6 SWP Settlement Agreements ............................................................................ 2-12 2.1.7 Daily Operations ................................................................................................ 2-12 2.2 Existing Regulations ....................................................................................................... 2-14 2.2.1 U.S. Army Corps of Engineers Permits ............................................................... 2-14 2.2.2 State Water Resources Control Board Water Rights and D-1641 ..................... 2-15 2.2.3 Federal Endangered Species Act ........................................................................ 2-15 2.2.4 California Endangered Species Act .................................................................... 2-15 2.3 Description of the Proposed Project .............................................................................. 2-16 2.3.1 OMR Management............................................................................................. 2-19 2.3.1.1 Onset of OMR Management ............................................................... 2-21 2.3.1.2 Real-Time OMR Limits and Performance Objectives .......................... 2-22 2.3.2 Minimum Export Rate ........................................................................................ 2-31 2.3.3 Delta Smelt Summer-Fall Habitat Action ........................................................... 2-31 2.3.3.1 Food Enhancement Summer-Fall Actions ........................................... 2-32 2.3.3.2 Delta Smelt Summer-Fall Habitat Action Adaptive Management Planning .............................................................................................. 2-33 2.3.4 Real-time Water Operations Process ................................................................ 2-34 Initial Study of the Long-Term Operation of the State Water Project i Table of Contents 2.3.4.1 Annual Process .................................................................................... 2-36 2.3.5 Monitoring Workgroups .................................................................................... 2-38 2.3.6 Four-Year Reviews ............................................................................................. 2-39 2.3.7 Drought and Dry Year Actions ........................................................................... 2-39 2.3.8 Continued Installation of South Delta Temporary Barriers ............................... 2-39 2.3.9 Barker Slough Pumping Plant Operations ......................................................... 2-40 2.3.9.1 Fish Screen Cleaning ........................................................................... 2-40 2.3.9.2 Sediment Removal .............................................................................. 2-41 2.3.9.3 Aquatic Weed Removal ....................................................................... 2-41 2.3.10 Clifton Court Forebay Operations ...................................................................... 2-41 2.3.10.1 Predator Management ....................................................................... 2-41 2.3.10.2 Aquatic Weed Removal and Disposal ................................................. 2-42 2.3.11 Skinner Fish Facility Improvements ................................................................... 2-49 2.3.12 Longfin Smelt Science Program ......................................................................... 2-49 2.3.13 Conduct Further Studies to Prepare for Delta Smelt Reintroduction from Stock Raised at the UC Davis Fish Conservation and Culture Laboratory ......... 2-49 2.3.14 Continue Studies to Establish a Delta Fish Species Conservation Hatchery ...... 2-51 2.3.15 Water Transfers ................................................................................................. 2-52 2.3.16 Adaptive Management Plan .............................................................................. 2-53 3 INITIAL STUDY CHECKLIST ..................................................................................................... 3-1 3.1 Aesthetics ......................................................................................................................... 3-1 3.1.1 Environmental Setting ......................................................................................... 3-1 3.1.1.1 Visual Character .................................................................................... 3-1 3.1.1.2 Wild and Scenic Rivers .......................................................................... 3-3 3.1.1.3 State Scenic Highways........................................................................... 3-3 3.1.2 Discussion............................................................................................................. 3-5 3.2 Agriculture and Forestry Resources ................................................................................. 3-6 3.2.1 Environmental Setting ......................................................................................... 3-6 3.2.1.1 Agricultural Resources .......................................................................... 3-6 3.2.1.2 Forestry Resources .............................................................................. 3-11 3.2.2 Discussion........................................................................................................... 3-13 3.3 Air Quality ...................................................................................................................... 3-15 3.3.1 Environmental Setting ....................................................................................... 3-15 3.3.1.1 Sacramento Valley Air Basin ............................................................... 3-17 3.3.1.2 San Francisco Air Basin ....................................................................... 3-17 3.3.1.3 San Joaquin Valley Air Basin ............................................................... 3-18 3.3.1.4 North Central Coast Air Basin ............................................................. 3-18 3.3.1.5 South Central Coast Air Basin ............................................................. 3-18 3.3.1.6 South Coast Air Basin .......................................................................... 3-19 3.3.1.7 San Diego Air Basin ............................................................................. 3-19 3.3.2 Discussion........................................................................................................... 3-19 Initial