Longitudinal Baseline Assessment of Salmonid Habitat Characteristics of the Shasta River, March through September, 2008 Jeffrey F. Mount, Peter B. Moyle, and Michael L. Deas, Principal Investigators Project Team: Carson A. Jeffres (Project Team Lead), Andrew L. Nichols, Ann D. Willis, Nicholas J. Corline, Aaron M. King, Robert A. Lusardi, Randy A. Dahlgren Report prepared for: United States Bureau of Reclamation Klamath Basin Area Office Center for Watershed Sciences University of California, Davis • One Shields Avenue • Davis, CA 95616 1 Table of Contents 1.0 Executive Summary................................................................................................ 4 2.0 Introduction........................................................................................................... 13 3.0 Background........................................................................................................... 14 4.0 Project Area .......................................................................................................... 15 4.1 Study Sites ........................................................................................................ 18 5.0 Baseline Assessment Overview............................................................................ 20 6.0 Geomorphology .................................................................................................... 20 6.1 Methods............................................................................................................. 21 6.2 Channel Gradient .............................................................................................. 21 6.3 Channel Cross-section Morphology ................................................................. 23 6.4 Bed Material...................................................................................................... 27 6.5 Summary........................................................................................................... 28 7.0 Hydrology............................................................................................................. 28 7.1 Methods............................................................................................................. 29 7.2 Data Analysis.................................................................................................... 32 7.3 Summary........................................................................................................... 35 8.0 Water Temperature ............................................................................................... 36 8.1 Methods............................................................................................................. 36 8.2 Data Analysis.................................................................................................... 37 8.3 Summary........................................................................................................... 51 9.0 Water Quality........................................................................................................ 52 9.1 Methods............................................................................................................. 52 9.2 Data Analysis.................................................................................................... 52 9.3 Summary........................................................................................................... 61 10.0 Aquatic Vegetation ............................................................................................... 61 10.1 Methods............................................................................................................. 62 10.2 Filamentous Algae ............................................................................................ 62 10.3 Aquatic Macrophytes........................................................................................ 63 10.4 Summary........................................................................................................... 65 11.0 Benthic Macroinvertebrates.................................................................................. 65 11.1 Methods............................................................................................................. 66 11.2 Taxonomic Determination ................................................................................ 66 11.3 Invertebrate Abundance.................................................................................... 66 11.4 Functional Feeding Groups (FFG).................................................................... 67 11.5 Summary........................................................................................................... 70 12.0 Salmonid Habitat Usage ....................................................................................... 70 12.1 Methods............................................................................................................. 71 12.2 Steelhead........................................................................................................... 71 12.3 Chinook............................................................................................................. 73 12.4 Coho.................................................................................................................. 73 12.5 Summary........................................................................................................... 75 13.0 Conclusion ............................................................................................................ 75 14.0 References............................................................................................................. 77 2 Acknowledgements The authors would like to acknowledge the following people who provided support, either directly or indirectly, to the Longitudinal Baseline Assessment of Salmonid Habitat Characteristics of the Shasta River. We would like to thank the U.S. Bureau of Reclamation Klamath Basin Area Office for their support of this research. This project would not have been possible if not for private land owners granting permission for researchers to study the Shasta River on their property. For access we would like to thank Dave Fontius, The Nature Conservancy, California, the Freeman Family, Bob and Laurie Manley, and Dave Webb for facilitating access. Bill Chesney, and Chris Adams and the California Department of Fish and Game for sharing their expertise on coho sampling, habitat assessment, and general life history, and fish collection in the Shasta River. We would also like to thank Joe Kiernan and Sue Maurer for study design and data collection; Ben Lamb for sample collection and tireless laboratory work; Robyn Suddeth, Nickilou Krigbaum, and Bruce Hammock for field data collection. Finally, we also appreciate Stacy Tanaka for her valuable editing suggestions. Recommended Citation: Nichols, A.L., C.A Jeffres, A.D. Willis, N.J. Corline, A.M. King, R.A. Lusardi, M.L. Deas, J.F. Mount, and P.B. Moyle. 2010. Longitudinal Baseline Assessment of Salmonid Habitat Characteristics of the Shasta River, March to September, 2008. Report prepared for: United States Bureau of Reclamation, Klamath Basin Area Office. 3 1.0 Executive Summary Introduction The Shasta River in Siskiyou County, California may be one of the Klamath River’s more exceptional tributaries (CDFG 2004, Deas 2004, NRC 2004) with regards to salmonid fish production. The river receives more than half of its annual flow from spring complexes that sustains year-round baseflow, and in summer provides cold water to support over-summering lifestages for coho salmon. These springs, fed by groundwater recharge from rainfall and snowmelt on Mount Shasta, are unique in that they are nutrient-rich and fuel highly productive aquatic food webs (Jeffres et al. 2009). These naturally occurring conditions provide a level of resilience to the Shasta River, suggesting a high potential for significant and immediate response to restoration and conservation actions supporting salmonids. Beginning in 2007, the University of California, Davis Center for Watershed Sciences (UC Davis), in cooperation with Watercourse Engineering, Inc. (Watercourse), completed a Year-In-The-Life physical and biological assessment of the Shasta River on The Nature Conservancy’s (TNC) Nelson Ranch (Jeffres et al. 2008). While this study concluded that the Shasta River had high potential to support salmonid populations, its observations were limited to a single, 8 kilometer river reach. This limited spatial assessment provided little indication of whether additional river reaches could also function as viable salmonid habitat, nor could it identify the potential range of underlying causes regarding the key impairment in the system: elevated water temperatures. This report extends the aforementioned baseline study of the Shasta River on the Nelson Ranch to five additional stream sites (Figure 1), including the principal cold-water, spring-fed tributary, Big Springs Creek. Findings are presented from data gathered over the 2008 field season (March through September). With two sites above and three sites below Nelson Ranch, this study presents the longitudinal physical and biological characteristics of the Shasta River and is the most comprehensive study to date of one of the more resilient tributaries in the Klamath River basin. The goal of this study was to provide the baseline information necessary to guide and evaluate restoration