Sacramento River Ecological Flows Study: State of the System Report Public Review Draft Prepared for The Nature Conservancy 500 Main Street Chico, CA 95928 by Stillwater Sciences 2855 Telegraph Avenue, Suite 400 Berkeley, CA 94705 Funded by CALFED Ecosystem Restoration Program November 2006 Suggested Citation: Stillwater Sciences. 2006. Sacramento River ecological flows study: State of the system report. Public Review draft. Prepared by Stillwater Sciences, Berkeley for The Nature Conservancy, California. Public Review Draft Sacramento River Ecological Flows Study State of the System Report Executive Summary This State of the System (SOS) Report is part of the Sacramento River Ecological Flows Study (the “Study”) initiated by The Nature Conservancy (TNC) in collaboration with ESSA Technologies, Stillwater Sciences, UC Davis, and UC Berkeley. The study area focuses on the mainstem Sacramento River corridor between Keswick Dam (RM 302) and Colusa (RM 143), including the channel, adjacent floodplain and riparian habitats, and off-channel water bodies. The overarching goal of the Study is to define how flow characteristics (e.g., the magnitude, timing, duration, and frequency) and associated management actions (such as gravel augmentation and changes in bank armoring) influence the creation and maintenance of habitats for a number of native species that occur in the Sacramento River corridor. This SOS Report is designed to provide resource managers and stakeholders with information and tools that will allow them to explore how changes in the pattern of flow releases can affect habitats in the Sacramento River. In this way, the SOS Report should provide useful information for water operations planning, restoration planning, species recovery planning, and storage investigations (e.g., for Shasta Dam enlargement and the Sites Reservoir construction) that focus on the Sacramento River. The information in this SOS Report builds on the earlier review of Sacramento River ecological flow issues conducted by Kondolf et al. (2000) for CALFED. The overall Sacramento River Ecological Flows Study is composed of four primary tasks. The first is this SOS Report, which is designed to distill existing information and present conceptual models and hypotheses about ecological flow needs in the Sacramento River. The second task is a series of field investigations and modeling applications designed to address data gaps and to refine estimates of ecological flow needs, including: • a gravel study designed to characterize gravel quality, mobilization, and routing; • an off-channel habitat study to estimate sediment deposition rates in, and resultant terrestrialization of, off-channel habitats; and • a bank study to examine the effects of natural and rip-rapped banks on aquatic habitat; • a numerical chute cutoff model to predict the flows required to create a chute cutoff; • a refined meander migration model; and • a sediment transport model that predicts the grain size distribution of both the surface and subsurface as a function of sediment supply and bed mobilization and scour. The third task of the Study is a decision analysis tool, referred to as the Sacramento River Ecological Flows Tool (SacEFT), which is designed to facilitate the analysis of ecological trade- offs associated with different suites of management actions (ESSA Technologies 2005, 2006). The fourth and final task component will be a Final Report that summarizes and synthesizes the results of the field investigations, modeling applications, and the application and recommended future uses of the SacEFT. The processes, habitats, and species of the Sacramento River have been the focus of much study, and the volume of available reports and datasets poses a challenge for synthesizing information and organizing a discussion of ecosystem components. Divergent conceptual models about process-habitat-biotic linkages complicate the process of summarizing what is known about the Sacramento River, and add to the challenge of evaluating alternative approaches for conserving and restoring the river ecosystem. To help overcome these challenges, this SOS Report discusses and analyzes the Sacramento River through the lens of six focal species. A focal species approach facilitates the exploration of linkages among ecosystem processes, resultant habitats, and biotic needs. For each focal species, we identify the different life history stages that occur in the Sacramento River, the habitats used by each of those life history stages, the ecological 22 November 2006 Stillwater Sciences O:\265.00 Sac_flows\MASTER\Public Review Draft_SOS Report.doc i Public Review Draft Sacramento River Ecological Flows Study State of the System Report processes that create and maintain those habitats, and the management actions (e.g., changes in the flow regime or bank protection) that influence those ecological processes and habitat conditions. The six focal species selected for this SOS Report are: • Chinook salmon (Oncorhynchus tshawytscha), • steelhead (Oncorhynchus mykiss), • green sturgeon (Acipenser medirostros), • bank swallow (Riparia riparia), • western pond turtle (Clemmys marmorata), and • Fremont cottonwood (Populus fremontii). This suite of focal species is not intended to be an exhaustive list of all conservation targets within the study area; rather, these six focal species provides a logical starting point for the Study while covering a wide range of habitats and ecological processes that occur in the Sacramento River. The loss and degradation of essential habitats in the Sacramento River corridor has generally reduced the river’s capacity to support native species, assemblages, and guilds. Habitat impacts are discussed further in section 3 of this SOS Report. The six focal species discussed in this SOS Report help to highlight the effects of land use changes and water supply development on the broader ecosystem, and they highlight some of the key resource management challenges in the Sacramento River system. Key findings and hypotheses of the SOS Report are summarized below, again using the focal species as a framework. Chinook Salmon While many rivers throughout the range of Chinook salmon (Oncorhynchus tshawytscha) support multiple runs, the Sacramento River is unique because it supports four distinct runs of Chinook salmon: winter-run, spring-run, fall-run, and late-fall-run. Winter-run Chinook salmon Though Chinook salmon range from California’s Central Valley up north to Alaska, and west to the Kamchatka peninsula in Asia, the Sacramento River supports the only known population of winter-run Chinook salmon. Winter-run Chinook salmon are unique because they spawn during summer months when air temperatures usually approach their yearly maximum. As a result, winter-run Chinook require stream reaches with cold water sources that will protect embryos and juveniles from the warm ambient conditions in the summer. In addition to cold water temperature in the summer, winter-run Chinook salmon also require relatively warm water temperatures in the winter to promote fast growth of salmon fry to enhance survival and production. We hypothesize that this unique combination of cold summer water temperatures and warm winter water temperatures explains why winter-run Chinook salmon are found only in the Sacramento River. We hypothesize that the life history strategy of winter-run Chinook salmon makes spawning habitat the most likely limiting factor for the population, both historically and currently, as discussed in section 4.2. Historically, the summer spawning and egg incubation stages restricted spawning to reaches that remain cold all summer, which were typically higher-elevation streams such as the McCloud River that were fed by cold water springs. These reaches are steeper and more confined than reaches downstream in the Sacramento Valley, so gravel resources were limited to small reaches and patches located within the predominately cobble and boulder bed. So, historically, winter-run Chinook were restricted not only in the linear extent of stream 22 November 2006 Stillwater Sciences O:\265.00 Sac_flows\MASTER\Public Review Draft_SOS Report.doc ii Public Review Draft Sacramento River Ecological Flows Study State of the System Report available to support spawning because of temperature constraints, but also in the amount of spawning gravel available to the population. Because winter-run Chinook spawn in late spring and early summer, their progeny emerge in late summer and early fall. No other salmonids in the Sacramento River emerge during this time, and most other juvenile salmonids outmigrate in the spring before summer water temperatures in the middle and lower Sacramento River become too warm. As a result, winter-run Chinook fry and juveniles had relatively little competition for rearing habitat in the fall and winter as they migrated downstream. The construction and operation of Shasta Dam contributed to an initial increase in the winter-run salmon population by expanding the cumulative spawning habitat available to the population, as discussed in section 4.2. However, the positive effect of Shasta Dam on winter-run Chinook salmon began to wane in the late 1970s and early 1980s, when escapements reached dangerously low levels. The drought of 1976-77 caused a precipitous decline in winter-run escapements when lethally warm water temperatures were released into the Sacramento River. We hypothesize that, in addition to this precipitous decline, the progressive loss of spawning habitat caused by bed coarsening