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Open Access Publications from the University of California


SFEWS provides credible scientific information on California's complex water issues, linking new science to policy with great effect. SFEWS retains a regional focus on the San Francisco Bay and the Sacramento–San Joaquin Delta, also known as the Bay–Delta watershed. At the heart of open access from the California Digital Library, SFEWS's scholarly output ranks #1 for the UC Davis Institute  of the Environment and ranks #3 campus wide.

Volume 18, Issue 3, 2020

Issue cover
Cover Caption: Salmon spawn in the Feather River gravel restoration project area during fall in Oroville, California on October 9, 2014 . Courtesy of Calif. Dept. of Water Resources; photo by Kelly M. Grow.


Policy and Program Analysis

Disease in Central Valley Salmon: Status and Lessons from Other Systems

Chinook Salmon (Oncorhynchus tshawytscha) are increasingly vulnerable to anthropogenic activities and climate change, especially at their most southern species range in California’s Central Valley. There is considerable interest in understanding stressors that contribute to population decline and in identifying management actions that reduce the impacts of those stressors. Along the west coast of North America, disease has been linked to declining numbers of salmonids and identified as a key stressor resulting in mortality. In the Central Valley, targeted studies have revealed extremely high prevalence of infectious agents and disease. However, there has been insufficient monitoring to understand the effect that disease may have on salmon populations. In order to inform future research, monitoring, and management efforts, a two-day workshop on salmon disease was held at UC Davis on March 14-15, 2018. This paper summarizes the science presented at this workshop, including the current state of knowledge of salmonid disease in the Central Valley and current and emerging tools to better understand its impacts on salmon. We highlight case studies from other systems where successful monitoring programs have been implemented. First, in the Klamath River where the integration of several data collection and modeling approaches led to the development of successful management actions, and second in British Columbia where investment in researching novel technologies led to breakthroughs in the understanding of salmon disease dynamics. Finally, we identify key information and knowledge gaps necessary to guide research and management of disease in Central Valley salmon populations.

Research Article

Reconsidering the Estimation of Salmon Mortality Caused by the State and Federal Water Export Facilities in the Sacramento–San Joaquin Delta, San Francisco Estuary

Combined water exports from Old River in the south end of California’s San Francisco Estuary (estuary) by state and federal pumping facilities entrain small fishes, including out-migrating juvenile salmon. Both export projects have fish salvage facilities that use behavioral barriers (louvers) in combination with screens to guide fish into collection areas from which they are trucked to release points in the western Delta. Sacramento River-origin Chinook Salmon are regularly taken in the projects’ fish salvage operations. Survival has been estimated within the boundaries of both intake structures, but not in Old River. Prevailing methods for estimating fish losses are based on studies of louver efficiency, near-field survival at the state facility, and assumed survival at the federal facility. The efficiency of the fish salvage operations is affected by several factors, including intake velocity, debris build-up on the louvers and trash racks, and by the omnipresence of predators in front of and within the fish guidance structures. Analysis of existing data suggests that under average conditions, juvenile salmon survive entrainment into the forebay of the state facility at a rate of less than 10%. There is no evidence for better survival at the federal facility. We found no data on predation outside of either the state’s forebay or the federal trash boom, structures which are separated by an approximately 2-km reach of Old River where predation on small fish is thought to be intense. We suggest an improvement to the existing loss estimation, and discuss some features of the studies needed to increase its accuracy and precision.


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Farm to Fish: Lessons from a Multi-Year Study on Agricultural Floodplain Habitat

Large areas of California’s historic floodplain have been separated from adjacent river channels by levee construction, allowing the development of an extensive agricultural industry. Based on successful partnerships between agriculture and conservation groups to support migrating waterfowl, we examined whether seasonally flooded rice fields could be modified to provide off-channel rearing habitat for juvenile Chinook Salmon Oncorhynchus tshawytscha. During winter and spring of 2012-2017, we conducted a series of experiments in Yolo Bypass and other regions of California’s Central Valley using hatchery Chinook Salmon as a surrogate for wild Chinook Salmon, the management target for our project. Overall, we found that seasonally flooded fields are highly productive, resulting in significantly higher levels of zooplankton and high Chinook Salmon growth rates as compared to the adjacent Sacramento River. We found similar results for multiple geographical areas in the Central Valley, and in different cover types, such as non-rice crops and fallow areas. Although field substrate type did not detectably affect fish growth and survival, connectivity with upstream and downstream areas appeared to drive fish occupancy, because rearing young salmon were generally attracted to inflow in the fields, and not all of the fish successfully emigrated off the fields without efficient drainage. In general, we faced numerous logistic and environmental challenges to complete our research. For example, periodic unmanaged floods in the Yolo Bypass made it difficult to schedule and complete experiments. During severe drought conditions, we found that managed agricultural habitats produced low and variable salmon survival results, likely because of periodically high temperatures and concentrated avian predation. In addition, our project required substantial land-owner time and effort to install and maintain experimental fields. Recent and future infrastructure improvements in Yolo Bypass could substantially improve options for experimental work and broaden efforts to enhance salmon habitat.

Forage Fish Larvae Distribution and Habitat Use During Contrasting Years of Low and High Freshwater Flow in the San Francisco Estuary

Recruitment of estuarine organisms can vary dramatically from year to year with abiotic and biotic conditions. The San Francisco Estuary (California, USA) supports a dynamic ecosystem that receives freshwater flow from numerous tributaries that drain one of the largest watersheds in western North America. In this study, we examined distribution and habitat use of two forage fish larvae of management interest, Longfin Smelt Spirinchus thaleichthys and Pacific Herring Clupea pallasii, during a low-flow and a high-flow year to better understand how their rearing locations (region and habitat) may affect their annual recruitment variability. During the low-flow year, larval and post-larval Longfin Smelt were distributed landward, where suitable salinity overlapped with spawning habitats. During the high-flow year, larval Longfin Smelt were distributed seaward, with many collected in smaller tributaries and shallow habitats of San Francisco Bay. Local spawning and advection from seaward habitats were speculated to be the primary mechanisms that underlie larval Longfin Smelt distribution during the high-flow year. Larval Pacific Herring were more abundant seaward in both years, but a modest number of larvae were also found landward during the low-flow year. Larval Pacific Herring abundance was lower overall in the high-flow year, suggesting advection out of the area or poor recruitment. Future monitoring and conservation efforts for Longfin Smelt and Pacific Herring should recognize that potential mechanisms underlying their recruitment can vary broadly across the San Francisco Estuary in any given year, which suggests that monitoring and research of these two species expand accordingly with hydrologic conditions that are likely to affect their spawning and larval rearing distributions.

  • 2 supplemental PDFs

Considerations for Multi-Species Fish Passage in California: A Literature Review

This review serves as a guide to improve multi-species fish passage. Human development along waterways in California during the last 160 years has adversely affected fish populations in many watersheds. Conflicts in water usage will only intensify with modern developments and population growth. Since most past fish-passage improvement efforts in California have focused on salmonids, I summarize the published studies and considerations that affect multi-species fish passage. To be effective, conditions in fishways need to meet the specific hydraulic requirements, as well as abilities, behavior, and size consideration for all fish species being considered. Turbulence, water depth, velocity, passage location, and design of a passage facility are essential elements to successful fish passage. Because of a lack of research on most of the native species, species-specific passage criteria are not fully defined, and it may be helpful to use data for physically similar, surrogate species found in similar habitats.