SFEWS Vol. 20, Issue 2 | June 2022
#ChinookSalmon #SacramentoSplittail #tidalmarsh #floodplain #openwater #drought #flood #juvenileproductionestimate #JPE #lifehistory #raceidentification #springrun #SacramentoRiver #CADelta #quantile #regressionforest #Steelhead #machinelearning #entrainmentloss #SanFrancisco #estuary #SFE #BayDelta #gillnet #gearselectivity #Drainage #waterquality #agriculturaldrainage #returnflow #diversions #Delta #island #groundwater #nitrogen #phosphorous #metals
Considerations for the Development of a Juvenile Production Estimate for Central Valley Spring-Run Chinook Salmon
Effective species management depends on accurate estimates of population size. There are, however, no estimates of annual juvenile production for Central Valley spring-run Chinook Salmon (“spring run”), a highly imperiled species in California, making it difficult to evaluate population status and effectively manage key issues such as entrainment of this species at water diversions. In recognition of this critical information gap, we initiated an effort to develop a juvenile production estimate (JPE) for spring run, defined here as an annual forecast of the number of juvenile Central Valley spring-run Chinook Salmon that enter the Sacramento–San Joaquin Delta (“Delta”) from the Sacramento Valley.
Machine Learning Forecasts to Reduce Risk of Entrainment Loss of Endangered Salmonids at Large-Scale Water Diversions in the Sacramento–San Joaquin Delta, California
Incidental entrainment of fishes at large-scale state and federal water diversion facilities in the Sacramento-San Joaquin Delta, California, can trigger protective management actions when limits imposed by environmental regulations are approached or exceeded. These actions can result in substantial economic costs, and likewise they can affect the status of vulnerable species. Here, we examine data relevant to water management actions during January–June; the period when juvenile salmonids are present in the Delta.
Gill Net Selectivity for Fifteen Fish Species of the Upper San Francisco Estuary
Gill-net size selectivity for 15 fish species occurring in the upper San Francisco Estuary was estimated from a data set compiled from multiple studies which together contained 7,096 individual fish observations from 882 gill net sets. The gill nets considered in this study closely resembled the American Fisheries Society’s recommended standardized experimental gill nets for sampling inland waters. Relationships between gill-net mesh sizes and the sizes for each fish species retained in them were estimated indirectly using generalized linear modeling and maximum likelihood.
Nutrient and Trace Element Contributions from Drained Islands in the Sacramento–San Joaquin Delta, California
Inventorying nutrient and trace element sources in the Sacramento-San Joaquin Delta (the Delta) is critical to understanding how changes—including alterations to point source inputs such as upgrades to the Sacramento Regional Wastewater Treatment Plant (SRWTP) and landscape-scale changes related to wetland restoration—may alter the Delta’s water quality. While island drains are a ubiquitous feature of the Delta, limited data exist to evaluate island drainage mass fluxes in this system. To better constrain inputs from island drains, we measured monthly discharge along with nutrient and trace element concentrations in island drainage on three Delta islands and surrounding rivers from June 2017 to September 2018.
Climate Change Impacts on San Francisco Estuary Aquatic Ecosystems: A Review ample header
In the San Francisco Estuary, signals of climate change are apparent in the long-term monitoring record. Here we synthesize current and potential future climate change effects on three main ecosystems (floodplain, tidal marsh, and open water) in the upper estuary and two representative native fishes that commonly occur in these ecosystems (anadromous Chinook Salmon, Oncorhynchus tshawytscha and estuarine resident Sacramento Splittail, Pogonichthys macrolepidotus).
Volume 11, Issue 1, 2013
Various schemes are often suggested to reverse the subsidence of lands below sea level in California’s Sacramento—San Joaquin Delta, an area protected by levees (dikes) that have significant probabilities of failure. Elementary modeling is used to estimate the probability distribution of land elevations at time of failure for 36 of these subsided islands, assuming a reasonable potential subsidence reversal rate. Given estimated annual probabilities of levee failure, elevation gains at this rate are not expected to exceed 1 to 2 m before flooding, which would be insufficient to restore most subsided islands to mean sea level (msl). However, under some circumstances 1- to 2-m gains are significant. A framework is introduced for evaluating islands as promising candidates for subsidence reversal based on elevation goals other than msl, as demonstrated though a hypothetical aquatic habitatexample. Here, we recommend relevant subsidence reversal strategies by comparing an elevation goal with each island’s anticipated flooded depth, and we prioritize islands for investment based on trade-offs between anticipated outcome and lost agricultural revenues. This approach might help integrate subsidence reversal activities into long-term Delta planning under a range of flooding, land use, and habitat management scenarios.
Ecosystem-scale Selenium Model for the San Francisco Bay-Delta Regional Ecosystem Restoration Implementation Plan
Environmental restoration, regulatory protections, and competing interests for water are changing the balance of selenium (Se) discharges to the San Francisco Bay–Delta Estuary (Bay–Delta). The model for Se described here as part of the Delta Regional Ecosystem Restoration Implementation Plan (DRERIP) draws both from the current state of knowledge of the Bay–Delta and of environmental Se science. It is an ecosystem-scale methodology that is a conceptual and quantitative tool to (1) evaluate implications of Se contamination; (2) better understand protection for fish and aquatic-dependent wildlife; and (3) help evaluate future restoration actions. The model builds from five basic principles that determine ecological risks from Se in aquatic environments: (1) dissolved Se transformation to particulate material Se, which is partly driven by the chemical species of dissolved Se, sets dynamics at the base of the food web; (2) diet drives bioavailability of Se to animals; (3) bioaccumulation differs widely among invertebrates, but not necessarily among fish; (4) ecological risks differ among food webs and predator species; and (5) risk for each predator is driven by a combination of exposures via their specific food web and the species’ inherent sensitivity to Se toxicity. Spatially and temporally matched data sets across media (i.e., water, suspended particulate material, prey, and predator) are needed for initiating modeling and for providing ecologically consistent predictions. The methodology, applied site-specifically to the Bay–Delta, includes use of (1) salinity-specific partitioning factors based on empirical estuary data to quantify the effects of dissolved speciation and phase transformation; (2) species-specific dietary biodynamics to quantify foodweb bioaccumulation; and (3) habitat use and life-cycle data for Bay–Delta predator species to illustrate exposure. Model outcomes show that the north Bay–Delta functions as an efficient biomagnifier of Se in benthic food webs, with the greatest risks to predaceous benthivores occurring under low flow conditions. Improving the characterization of ecological risks from Se in the Bay–Delta will require modernization of the Se database and continuing integration of biogeochemical, ecological, and hydrological dynamics into the model.
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Migration Patterns of Juvenile Winter-run-sized Chinook Salmon (Oncorhynchus tshawytscha) through the Sacramento–San Joaquin Delta
The decline of Sacramento River winter-run Chinook salmon (Oncorhynchus tshawytscha) remains one of the major water management issues in the Sacramento River. Few field studies have been published on winter-run, leaving gaps in our knowledge about their life history. This is especially true in the Sacramento–San Joaquin Delta, which provides essential rearing and migratory habitats for winter-run, and serves as the center of water operations for California. Using long-term monitoring data that identified winter-run-sized fish (“winter-run”) using length-at-date criteria, we examined patterns of juvenile migration in terms of geographic distribution, timing, numbers, and residence times. We analyzed the role of flow, turbidity, temperature, and adult escapement on the downstream movement (“migration”) of winter-run. Winter-run passed Knights Landing (rkm 144 or 51 rkm upstream of the Delta) between October and April, with substantial variation in peak time of entry that was strongly associated with the first high flows of the migration season. Specifically, the first day of flows of at least 400 m3 s-1 at Wilkins Slough (rkm 190) coincided with the first day that at least 5% of the annual total catch was observed at Knights Landing. While the period during which winter-run left the Delta spanned several months based on Chipps Island (rkm 29) catch data, the median catch typically occurred over a narrow window in March. Differences in timing of cumulative catch at Knights Landing and Chipps Island indicate that apparent residence time in the Delta ranges from 41 to 117 days, with longer apparent residence times for juveniles arriving earlier at Knights Landing. We discuss the potential importance of the Yolo Bypass floodplain as an alternative rearing and migratory corridor, contingent on the timing, duration, and magnitude of floodplain inundation. These results carry implications for habitat restoration and management of Sacramento River flows.
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