Merced River Water Temperature Feasibility Investigation Reconnaissance Report December 29, 2003 Prepared for: The U.S. Fish and Wildlife Service Anadromous Fish Restoration Program Prepared by: David A. Vogel, Senior Scientist Natural Resource Scientists, Inc. P.O. Box 1210 Red Bluff, CA 96080 TABLE OF CONTENTS Introduction and Background....................................................................................................................................1 The Merced River Development Project ...................................................................................................................4 History ......................................................................................................................................................................4 Description of Project Facilities..............................................................................................................................6 New Exchequer Dam/Lake McClure ...................................................................................................................6 McSwain Dam and Reservoir...............................................................................................................................7 Merced Falls Dam and Forebay...........................................................................................................................7 Crocker-Huffman Dam and Reservoir.................................................................................................................8 Merced River Hatchery.........................................................................................................................................8 Water Project Operating Strategies, Requirements, and Agreements .................................................................10 U.S. Army Corps of Engineers Flood Control ....................................................................................................10 Federal Energy Regulatory Commission (FERC) ..............................................................................................12 Davis-Grunsky Agreement ...................................................................................................................................12 Cowell Agreement Diversions...............................................................................................................................13 Stevinson Diversions..............................................................................................................................................13 Merced ID Main Canal and Northside Canal Diversions ..................................................................................14 Vernalis Adaptive Management Plan and San Joaquin River Agreement.......................................................14 Merced River Adaptive Management Plan (MRAMP)......................................................................................17 Additional 12,500 Acre-Feet October Flows .......................................................................................................17 Miscellaneous Water Withdrawals ......................................................................................................................17 Lake Don Pedro Community Services District ..................................................................................................17 Mariposa County Public Utilities District..........................................................................................................17 Merced ID Campground Facilities ....................................................................................................................18 Accretions/Depletions .........................................................................................................................................18 Merced Water Supply Plan...................................................................................................................................18 Historical Water Year Classifications......................................................................................................................19 Recent Historical Operations of the Merced River Development Project............................................................20 Merced River Simulation Model (MRSIM) ........................................................................................................21 Main Canal Diversions..........................................................................................................................................23 Northside Canal Diversions ..................................................................................................................................23 Stream Flow, Reservoir, and Weather Records......................................................................................................24 Lower Merced River Chinook Salmon Phenology and Monitoring......................................................................42 Chinook Salmon Phenology..................................................................................................................................42 Salmon Monitoring................................................................................................................................................43 CDFG Annual Spawning Ground Surveys........................................................................................................43 CDFG/Merced ID Memorandum of Understanding Biological Studies ..........................................................44 Juvenile Salmon Outmigration ..........................................................................................................................47 Merced River Corridor Restoration Plan...........................................................................................................47 USFWS AFRP Projects......................................................................................................................................47 Water Temperature Monitoring .........................................................................................................................48 Water Temperature Models .....................................................................................................................................65 Merced River and Lake McClure Water Temperature Model .........................................................................65 Lake McClure Temperature Model....................................................................................................................65 Merced River Temperature Model .....................................................................................................................66 Alternative Flow Analyses..................................................................................................................................67 Proposed Expanded Merced River and Reservoirs Water Temperature Models ...........................................68 Acknowledgements ....................................................................................................................................................73 References ..................................................................................................................................................................74 __________________________________________________________________________________________ Merced River Water Temperature Feasibility Investigation – Reconnaissance Report Page i LIST OF FIGURES Figure 1. The Merced River and its four dams. ............................................................................................................2 Figure 2. Longitudinal schematic of New Exchequer Dam on the Merced River .......................................................6 Figure 3. Longitudinal schematic of McSwain Dam on the Merced River .................................................................7 Figure 4. Flood control storage space criteria for Lake McClure/New Exchequer Dam............................................11 Figure 5. Classification of water year types for the San Joaquin River basin.............................................................20 Figure 6. Historical monthly average flow (acre-feet) downstream of Merced Falls Dam prior to the construction of Exchequer Dam, during Exchequer Dam operations, and after construction of New Exchequer Dam...............21 Figure 7. Merced River Simulation Model (MRSIM) schematic including description of nodes .............................22 Figure 8. Historical water diversions (acre-feet) into Merced ID’s Main Canal. .......................................................23 Figure 9. Historical water diversions (acre-feet) into Merced ID’s Northside Canal for the period 1970 through 1999. ....................................................................................................................................................................24 Figure 10. Location of stations in the Merced River watershed downstream of New Exchequer Dam. ....................25 Figure 11. Weather data stations located near the Merced River watershed. .............................................................26 Figure 12. Freshwater life history periodicity for San Joaquin River basin fall-run Chinook salmon. ......................43 Figure 13. Locations of water temperature