San Francisco Estuary and Watershed Science

Climate change is intensifying the effects of multiple interacting stressors on aquatic ecosystems worldwide. 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). Based on our review, we found that the estuary is experiencing shifting baseline environmental conditions, amplification of extremes, and restructuring of physical habitats and biological communities. We present priority topics for research and monitoring, and a conceptual model of how the estuary currently functions in relation to climate variables. In addition, we discuss four tools for management of climate change effects: regulatory, water infrastructure, habitat development, and biological measures. We conclude that adapting to climate change requires fundamental changes in management.

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. This metric would allow for a more robust scientific assessment of the population, which is needed to effectively manage water to reduce effects on spring run, a key condition of state permit requirements. To help guide this effort, we organized a workshop for stake-holders, managers, and scientists to review some of the key aspects of spring-run biology, examine the management and conservation importance of a JPE, identify knowledge gaps, introduce new tools, and discuss alternative approaches to forecasting the number of spring run emigrating from the Sacramento River drainage and into the Delta. This paper summarizes the spring-run biology, monitoring, and emergent methods for assessment considered at the workshop, as well as the guiding concepts identified by workshop participants necessary to develop a JPE for spring-run Chinook Salmon.

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. We use a quantile regression forest approach to create a risk forecasting tool, which can inform adjustments of diversions based on near real-time predictions. Models were trained using historical entrainment data (Water Years 1999–2019) for Sacramento River winter-run Chinook Salmon or Central Valley Steelhead and a suite of environmental and water operations metrics. A range of models was developed; their performance was evaluated by comparison of a quantile loss metric. The models were validated through examination of partial dependence plots, cross-validation procedures, and further evaluated through WY 2019 pilot testing, which integrated real-world uncertainty in environmental parameters into model predictions. For both species, the strongest predictor of loss was the previous week’s entrainment loss. In addition, risk increased with higher water exports and more negative Old and Middle Rivers (OMR) flows. Point estimates of loss were modestly correlated with observations (R2 0.4 to 0.6), but the use of a quantile regression approach provided reliable prediction intervals. For both species, the predicted 75th quantile appears to be a robust and conservative estimator of entrainment risk, with overprediction occurring in fewer than 20% of cases. This quantile balances the magnitude of over- and under-prediction and results in a low probability (< 5% of predictions) of unexpected high-take events. These models, and the web-based application through which they are made accessible to non-technical users, can provide a useful and complementary approach to the current system of managing entrainment risk.

Gill-net size selectivity for fifteen 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. Selectivity curves are provided for each species to inform researchers about population characteristics of fishes sampled with similar gill nets.

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. These data were used to calculate island-level fluxes and then upscaled to estimate Delta-wide contributions from island drains. Based on these results, we present (1) new estimates of gross and net nutrient and trace element fluxes from Delta island drains, and (2) concomitant N stable isotope data to improve our understanding of island N cycling. Over 60% of nearly all island drainage gross nutrient and trace element loads occurred in winter and spring. Upscaled island drainage net annual total nitrogen (TN), total dissolved nitrogen (TDN), and NH4+ loads comprised an estimated 9%, 7%, and 4%, respectively, of annual inputs to this system in 2018, before the SRWTP upgrade. Under a post-upgrade scenario, we estimated net annual island drainage TDN contributions to increase to 11% and NH4+ contributions to 45% of total Delta inputs as the SRWTP NH4+ load diminished to near zero. Our results suggest that island drainage is a measurable N source that has likely become increasingly important now that the SRWTP upgrade is complete. With over 200 potential active outfalls, these inputs may affect aquatic biogeochemical cycling in many regions of the Delta, especially in areas with long residence times.