Southern California Steelhead Passage Assessment, Lower Santa Margarita River, California and CUP Surface Water Availability Analysis (TM 1.1) April 27, 2012 Prepared for: United States Bureau of Reclamation Fallbrook Public Utilities District United States Marine Corps Base Camp Pendleton Prepared by: Stetson Engineers, Inc. San Rafael, CA with fish biology support from: Cardno ENTRIX Sacramento, CA TABLE OF CONTENTS SECTION PAGE NO. TABLE OF CONTENTS ...................................................................................................................... I LIST OF FIGURES ........................................................................................................................... III LIST OF TABLES ............................................................................................................................. IV LIST OF APPENDICES ..................................................................................................................... VI ACRONYM AND ABBREVIATION LIST ........................................................................................... VII EXECUTIVE SUMMARY .................................................................................................................. IX 1.0 INTRODUCTION AND BACKGROUND ................................................................................... 1-1 1.1 STUDY AUTHORITY AND PURPOSE .........................................................................................................1-1 1.2 REPORT CONTENTS ................................................................................................................................1-1 1.3 STUDY LOCATION ..................................................................................................................................1-2 1.4 PROJECT BACKGROUND .........................................................................................................................1-2 1.5 EXISTING FACILITIES AND OPERATIONS ON CPEN ................................................................................1-4 1.5.1Existing Facilities ..........................................................................................................................1-4 1.5.2Historical Groundwater Pumping and Surface Diversions ...........................................................1-6 1.6 SANTA MARGARITA RIVER CUP ...........................................................................................................1-7 1.6.1Project Facilities ............................................................................................................................1-7 1.6.2Project Groundwater Pumping and Surface Diversions ................................................................1-9 1.7 LEGAL HISTORY AND HISTORICAL WATER RIGHTS INVENTORY ......................................................... 1-10 1.7.11940 Stipulated Judgment ............................................................................................................ 1-10 1.7.2United States v Fallbrook Public Utility District (Case 1247) .................................................... 1-11 1.7.3Historical Water Rights Inventory ............................................................................................... 1-12 2.0 SOUTHERN CALIFORNIA STEELHEAD TAXONOMY,LIFE HISTORY AND HABITAT .......... 2-1 2.1 CONSERVATION STATUS ........................................................................................................................2-1 2.2 SPECIES DESCRIPTION ............................................................................................................................2-2 2.3 LIFE HISTORY ........................................................................................................................................2-2 2.4 STEELHEAD HABITAT ............................................................................................................................2-4 2.4.1Migration Habitat ..........................................................................................................................2-4 2.4.2Spawning and Rearing Habitat ......................................................................................................2-5 2.5 AVAILABLE HABITAT ON THE SANTA MARGARITA RIVER .....................................................................2-6 2.6 STEELHEAD OCCURRENCE IN THE SANTA MARGARITA RIVER ...............................................................2-8 3.0 FIELD SURVEY AND HYDRAULIC MODELING .................................................................... 3-1 3.1 TOPOGRAPHIC,GEOMORPHIC AND BIOLOGICAL CHARACTERIZATION ...................................................3-1 3.1.1Longitudinal Profile Survey to Identify Potential Fish Passage Barriers ......................................3-1 3.1.2Biological Survey and Habitat Characterization ...........................................................................3-2 3.1.3Characterization of Three Potential Critical Passage Sites ..........................................................3-3 3.2 HEC-RAS HYDRAULIC MODEL DEVELOPMENT ....................................................................................3-4 3.2.1HEC-RAS Model Calibration and Verification..............................................................................3-5 3.2.2HEC-RAS Model Simulations ........................................................................................................3-6 4.0 LOWER SANTA MARGARITA RIVER HYDROLOGY ............................................................ 4-1 4.1 CLIMATE AND PRECIPITATION ...............................................................................................................4-1 Stetson Engineers Inc./Cardno ENTRIX i April 27, 2012 Lower SMR Fish Passage Assessment 4.2 STREAMFLOW RECORDS AND DATA ......................................................................................................4-3 4.3 PREVIOUS HYDROLOGIC MODELING INVESTIGATION –INDICATORS OF HYDROLOGIC ALTERATION (IHA) .....................................................................................................................................................4-4 4.4 HYDROLOGIC PERIOD OF RECORD .........................................................................................................4-6 4.5 HYDROLOGIC PERIODS OF INVESTIGATION ............................................................................................4-7 4.5.1Hydrology during the Unimpaired Period .....................................................................................4-8 4.5.2Hydrology during the Recent Historical Period ............................................................................4-9 4.5.3Hydrology during the Future Project Period ............................................................................... 4-11 4.6 GROUNDWATER HYDROGEOLOGY ....................................................................................................... 4-12 4.6.1Camp Pendleton Groundwater Model and Development ............................................................ 4-12 4.6.2Model Structure and MODFLOW Stream Package ..................................................................... 4-13 4.6.3Groundwater Simulation for Unimpaired Period ........................................................................ 4-14 4.6.4Groundwater Simulation for Recent Historical Period ............................................................... 4-15 4.6.5Groundwater Simulation for Future Project Period .................................................................... 4-17 5.0 RESULTS OF ANADROMOUS FISH PASSAGE ASSESSMENT ................................................. 5-1 5.1 HABITAT CHARACTERISTICS WITHIN THE LOWER SANTA MARGARITA RIVER ......................................5-1 5.2 RESULTS OF THE CHANNEL HABITAT RECONNAISSANCE SURVEY .........................................................5-1 5.3 RESULTS OF THE HYDRAULIC ANALYSIS FOR FISH PASSAGE .................................................................5-2 5.3.1Passage Criteria ............................................................................................................................5-2 5.3.2Hydraulic Analysis Procedures ......................................................................................................5-3 5.3.3Determination of Minimum Fish Passage Flow Rates ...................................................................5-3 5.4 MAGNITUDE OF FLOW AT CRITICAL PASSAGE SITES .............................................................................5-4 5.4.1Unimpaired Flow Magnitude .........................................................................................................5-5 5.4.2Recent Historical Flow Magnitude ................................................................................................5-5 5.4.3Future Project Flow Magnitude .....................................................................................................5-6 5.5 PATTERN OF MINIMUM PASSAGE FLOW RATES .....................................................................................5-7 5.5.1Pattern of Flow during the Unimpaired Period .............................................................................5-7 5.5.2Pattern of Flow during Recent Historical Period ..........................................................................5-8 5.5.3Pattern of Flow during Future Project Period ..............................................................................5-9