SUMMARY AND ANALYSIS OF ANNUAL FISHERY MONITORING IN THE LOWER SANTA YNEZ RIVER 1993-2004 SANTA YNEZ RIVER ADAPTIVE MANAGEMENT COMMITTEE JUNE 2009 SUMMARY AND ANALYSIS OF ANNUAL FISHERY MONITORING IN THE LOWER SANTA YNEZ RIVER 1993 – 2004 Prepared by: Santa Ynez River Technical Advisory Committee, Adaptive Management Committee Contact Information: Timothy H. Robinson, Ph.D. Sr. Resource Scientist, Cachuma Conservation Release Board (CCRB) 3301 Laurel Canyon Road Santa Barbara, CA 93105-2017 805-569-1391 June 30, 2009 TABLE OF CONTENTS Executive Summary............................................................................................................................... ES-1 Section 1: Introduction.....................................................................................................................1-1 1.1 Introduction .........................................................................................................1-1 Section 2: Santa Ynez River Hydrology..........................................................................................2-1 2.1 Introduction2-1 2.2 Hydrologic Monitoring Data.................................................................................2-1 2.2.1 Daily Monitoring Data.............................................................................2-1 2.2.2 Instantaneous Flow Measurements.......................................................2-1 2.3 Results ................................................................................................................2-2 2.3.1 Precipitation ...........................................................................................2-2 2.3.2 Lake Cachuma Operations ....................................................................2-3 2.3.3 Flow in the Mainstem .............................................................................2-5 2.3.4 Flow in the Tributaries............................................................................2-6 2.3.5 Breaching of the Santa Ynez Lagoon ....................................................2-7 Section 3: Water Quality Conditions...............................................................................................3-1 3.1 Introduction .........................................................................................................3-1 3.2 Factors Affecting Temperature and Water Quality .............................................3-2 3.3 Water Quality Monitoring Methods......................................................................3-3 3.3.1 Lake Cachuma Temperature and Dissolved Oxygen Profiles...............3-3 3.3.2 Santa Ynez River Mainstem and Tributaries Water Temperatures.......3-4 3.3.3 Diel Water Quality Measurements .........................................................3-4 3.3.4 USGS Water Quality Measurements .....................................................3-4 3.3.5 Lagoon Water Quality Measurements ...................................................3-5 3.4 Results ................................................................................................................3-5 3.4.1 Air Temperatures ...................................................................................3-5 3.4.2 Water Quality within Lake Cachuma......................................................3-6 3.4.3 Water Quality within the Mainstem Lower Santa Ynez River ................3-7 3.5 Tributary Water Temperatures..........................................................................3-10 3.5.1 Hilton Creek .........................................................................................3-10 3.5.2 Quiota Creek........................................................................................3-11 3.5.3 Nojoqui Creek ......................................................................................3-11 3.5.4 Salsipuedes Creek...............................................................................3-11 3.5.5 El Jaro Creek .......................................................................................3-12 3.5.6 San Miguelito Creek.............................................................................3-12 3.6 Lagoon Water Quality .......................................................................................3-13 3.7 Findings of the Water Quality Monitoring Program...........................................3-14 3.7.1 Lake Cachuma.....................................................................................3-14 3.7.2 Mainstem Water Temperature .............................................................3-15 3.7.3 Mainstem Dissolved Oxygen ...............................................................3-16 3.7.4 Santa Ynez River Lagoon....................................................................3-16 3.7.5 Water Temperatures within the Tributaries..........................................3-17 1993 – 2004 Lower Santa Ynez River Synthesis Report June 2009 i Table of Contents Section 4: Habitat Characteristics...................................................................................................4-1 4.1 Introduction .........................................................................................................4-1 4.2 Methods ..............................................................................................................4-1 4.2.1 Inventory of Passage Barriers and Impediments...................................4-2 4.2.2 Habitat Mapping of Stream Channel Characteristics.............................4-3 4.2.3 Aquatic Macroinvertebrate Reconnaissance Survey.............................4-5 4.3 Results and Discussion.......................................................................................4-6 4.3.1 Passage Barrier Assessment.................................................................4-7 4.3.2 Habitat Characteristics...........................................................................4-9 4.3.3 Aquatic Macroinvertebrate Survey.......................................................4-13 4.3.4 Illegal Harvest (Poaching)....................................................................4-16 4.4 Findings of the 1993-2004 Habitat Monitoring Program...................................4-17 Section 5: Fishery Resources .........................................................................................................5-1 5.1 Introduction .........................................................................................................5-1 5.2 Methods ..............................................................................................................5-3 5.2.1 General ..................................................................................................5-3 5.2.2 Migrant Trapping....................................................................................5-3 5.2.3 Snorkel Surveys.....................................................................................5-4 5.2.4 Redd Surveys.........................................................................................5-5 5.2.5 Lagoon Trapping....................................................................................5-6 5.3 Results ................................................................................................................5-6 5.3.1 Migrant Trapping....................................................................................5-7 5.3.2 Snorkel Surveys...................................................................................5-14 5.3.3 Redd Surveys.......................................................................................5-19 5.3.4 Lagoon Trapping..................................................................................5-21 5.3.5 Electrofishing Surveys .........................................................................5-21 5.4 Findings of the 1993-2004 Fishery Monitoring Program ..................................5-22 5.4.1 Steelhead/Rainbow Trout Distribution in the LSYR.............................5-22 5.4.2 Ecological Factors................................................................................5-22 5.4.3 Steelhead/Rainbow Trout in the Tributaries ........................................5-23 5.4.4 Community Structure/Predation...........................................................5-23 Section 6: Status of Management Actions .....................................................................................6-1 6.1 Introduction .........................................................................................................6-1 6.2 Mainstem River Supplemental Flow Releases ...................................................6-3 6.2.1 Rearing/Target Baseflows for Rearing Habitat ......................................6-3 6.3 Hilton Creek Projects ..........................................................................................6-4 6.3.1 Hilton Creek Watering System...............................................................6-5 6.3.2 Riparian Vegetation Enhancement ........................................................6-6 6.3.3 Passage Barrier Fixes............................................................................6-6 6.3.4 Channel Extension.................................................................................6-7 6.4 Salsipuedes Creek Fish Passage Projects.........................................................6-8 6.4.1 Highway 1 Bridge Passage Project .......................................................6-8 6.4.2 Jalama Road Bridge Fish Passage