Final ReP-ort Hydrological and Biological Support to Lower Santa Margarita River Watershed Monitoring Program Water Years 2008-2009 February 21. 2010 Prepared for United States Bureau of Reclamation ~~~pr.RTMENT OF THE INTE:o ·'". .,. eea..._..~o.. Southern California Area Office, Temecula, California FINAL REPORT HYDROLOGICAL AND BIOLOGICAL SUPPORT TO LOWER SANTA MARGARITA RIVER WATERSHED MONITORING PROGRAM WATER YEARS 2008-2009 TASK ORDER: 07PE308086 GSA CONTRACT: GS-10F-0404P PREPARED FOR UNITED STATES BUREAU OF RECLAMATION SOUTHERN CALIFORNIA AREA OFFICE TEMECULA, CALIFORNIA PREPARED BY SCOTT THOMAS, JOEL BARNARD, STEPHANIE GINDLESPERGER, MOLLY PALMER, KEN REICH, STEVE REICH STETSON ENGINEERS INC. SAN RAFAEL, CA AND MATT RAHN, ROBERT CHAPMAN SAN DIEGO STATE UNIVERSITY SAN DIEGO, CA FEBRUARY 21, 2010 TABLE OF CONTENTS SECTION PAGE NO. EXECUTIVE SUMMARY ................................................................................................................XVI 1.0 INTRODUCTION AND BACKGROUND................................................................................... 1-1 1.1 STUDY DESCRIPTION................................................................................................................................. 1-1 1.2 STUDY AREA............................................................................................................................................. 1-2 1.3 GENERAL WATERSHED CHARACTERISTICS ............................................................................................... 1-2 1.3.1 Geologic Setting............................................................................................................................ 1-3 1.3.2 Climate.......................................................................................................................................... 1-3 1.3.3 Streamflow.................................................................................................................................... 1-5 1.3.4 Habitat and Species....................................................................................................................... 1-6 1.3.4.1 Southern California Riparian Forest..............................................................................................1-7 1.3.4.2 Southern California Coastal Stream ..............................................................................................1-8 1.3.4.3 Riparian Forest, Coastal Sage Scrub and Chaparral Ensemble ....................................................1-8 1.3.4.4 Coastal Wetland and Dune Ensemble ............................................................................................1-8 1.4 WATER QUALITY ...................................................................................................................................... 1-8 1.4.1 Sampled Constituent Sources.......................................................................................................1-10 1.4.1.1 Urban Runoff................................................................................................................................1-10 1.4.1.2 Agriculture ...................................................................................................................................1-11 1.4.1.3 Reclaimed Water ..........................................................................................................................1-11 1.4.2 Document Review and Historical Data Collection ......................................................................1-11 1.4.3 Water Quality Thresholds and Basin Plan Limits ........................................................................1-13 1.5 CWRMA .................................................................................................................................................1-18 1.5.1 Background..................................................................................................................................1-18 1.5.2 Simulation of Natural Flow..........................................................................................................1-20 1.5.3 Summary of CWRMA Releases ..................................................................................................1-20 2.0 METHODS............................................................................................................................ 2-1 2.1 CONCEPTUAL MODELS.............................................................................................................................. 2-1 2.2 WATER QUALITY COLLECTION METHODS ................................................................................................ 2-4 2.2.1 Approach to Sampling .................................................................................................................. 2-4 2.2.2 Locations of Sampling .................................................................................................................. 2-4 2.2.3 Timing of Sampling ...................................................................................................................... 2-5 2.2.4 Organization of Sample Suites...................................................................................................... 2-7 2.2.5 Sampling Methods .......................................................................................................................2-10 2.2.5.1 Field Measurements of Water Quality..........................................................................................2-10 2.2.5.2 Sampling for Laboratory Analysis................................................................................................2-10 2.2.5.3 Continuous Monitoring ................................................................................................................2-10 2.2.5.4 Methods for Macrophyton and Periphyton Sample Collection.....................................................2-11 2.2.6 Quality Assurance/Quality Control (QA/QC)..............................................................................2-11 2.2.7 Methods for Data Cataloging, Access and Control......................................................................2-12 2.3 FLOW EXPERIMENT METHODS .................................................................................................................2-12 2.3.1 Modification of CWRMA Flows .................................................................................................2-13 2.3.2 Flow Measurements .....................................................................................................................2-13 2.3.3 Cross-Sections..............................................................................................................................2-14 2.3.4 Pool Measurements......................................................................................................................2-14 2.3.5 Rapid Biological Assessment Protocol ........................................................................................2-15 3.0 ANALYSIS OF WATER QUALITY......................................................................................... 3-1 3.1 WATER QUALITY RESULTS ....................................................................................................................... 3-1 Stetson Engineers Inc. ii Final Report Santa Margarita River February 21, 2010 Hydrological and Biological Support 3.1.1 Field Measurements of Water Quality .......................................................................................... 3-1 3.1.2 Laboratory Results of Water Quality Samples.............................................................................. 3-2 3.1.2.1 Adobe Creek ...................................................................................................................................3-5 3.1.2.2 Arroyo Seco and Cole Creek ..........................................................................................................3-5 3.1.2.3 Roblar Creek at Falls.....................................................................................................................3-5 3.1.2.4 Santa Margarita River at FPUD Sump near Fallbrook .................................................................3-5 3.1.2.5 Santa Margarita River at MWD Crossing (SMER) ........................................................................3-5 3.1.2.6 Santa Margarita River near Temecula...........................................................................................3-6 3.1.2.7 Santa Margarita River at Ysidora ..................................................................................................3-6 3.1.2.8 De Luz Creek near De Luz .............................................................................................................3-6 3.1.2.9 Devils Creek at Via Novilla, SMER................................................................................................3-6 3.1.2.10 Fallbrook Creek near Fallbrook ....................................................................................................3-6 3.1.2.11 Rainbow Creek ...............................................................................................................................3-7 3.1.2.12 RCWD CWRMA Outfall .................................................................................................................3-7 3.1.2.13 Sandia Creek near Fallbrook .........................................................................................................3-7