San Francisco Estuary and Watershed Science

Zooplankton density and community composition in estuaries can be affected by variation in freshwater inputs, with important implications for higher trophic levels. In the San Francisco Estuary, management agencies have initiated autumn flow augmentations in the form of changes to reservoir releases or to exported water from the South Delta to increase and improve available habitat for endangered Delta Smelt, Hypomesus transpacificus, during the season when their body condition most influences fecundity. Autumn flow augmentation only occurs in years with higher precipitation, effectively moving the Low-Salinity Zone (LSZ) downstream to key foraging habitats for Delta Smelt in Suisun Bay and Suisun Marsh. To assess whether augmented flow enhanced prey resources for Delta Smelt, we compared autumn zooplankton abundance, biomass, spatial distribution, and community composition in years when flow was augmented (2017, 2019) with reference years when flow was not augmented (2018, 2020). In augmented years, we detected higher total zooplankton abundance and altered community composition in Suisun Bay and Suisun Marsh. Increased freshwater in these regions was associated with higher abundance of Pseudodiaptomus forbesi, a preferred prey of Delta Smelt, while species associated with higher salinities—Acartiella sinensis and Tortanus dextrilobatus—were less abundant. Thus, autumn flow augmentations can influence foraging habitat and prey availability for Delta Smelt, underscoring the complex responses of estuarine zooplankton communities to changes in response to flow and salinity regimes. This study is management- relevant because it shows that important Delta Smelt prey items increase in downstream regions when X2 is lower. Whether that results in a response in Delta Smelt abundance remains to be seen.

The South Bay Salt Pond Restoration Project aims to restore many former salt production ponds, now managed for wildlife and water quality, to tidal marsh. However, because managed ponds support large densities of breeding waterbirds, reduction of pond habitat may influence breeding waterbird distribution and abundance. We investigated habitat use associated with breeding, feeding, and roosting behaviors during the breeding season for American Avocets (Recurvirostra americana), Black-necked Stilts (Himantopus mexicanus), Forster’s Terns (Sterna forsteri), and Caspian Terns (Hydroprogne caspia) in south San Francisco Bay in 2019 after substantial tidal marsh restoration, and compared results to a 2001 survey (before restoration). In 2019, managed ponds (26% of currently available habitat) were selected by waterbirds engaged in breeding behaviors (> 39% of observations), foraging (> 42%), and roosting (> 73%). Waterbirds avoided tidal habitats (43% of available habitat), comprising < 17% of observations of breeding behavior, < 28% of foraging observations, and < 13% of roosting observations. Waterbird densities increased in managed ponds between 2001 and 2019, and decreased in active salt ponds, especially among feeding Avocets (92% decrease) and Stilts (100% decrease). Islands were important for waterbirds observed breeding and roosting (45% of Avocet and 53% of Tern observations). Avocets and Stilts fed primarily on wet bare ground (65% and 58%, respectively), whereas feeding Forster’s Terns and Caspian Terns used mostly open water (82% and 93%, respectively). Within ponds, Avocets were associated with islands (131 m closer than expected). Stilts and Forster’s Terns were also associated with islands (68 m and 161 m closer than expected), except when feeding (1 m closer and 90 m farther than expected). Avocets and Stilts were associated with pond levees (39 m and 41 m closer than expected), but Forster’s Terns were not (9 m closer than expected). Our results emphasize the importance of managed ponds for breeding and foraging waterbirds, including islands for breeding and roosting and levees for foraging.

The deviation of specific electrical conductance (EC) from conservative mixing behavior is well-established in the scientific literature. This principle is based on the observation that, as salt concentration in a water sample increases, the mobility of individual ions in the sample decreases, and thus their ability to conduct electricity decreases. Despite this fact, some commonly used models for salinity transport in the San Francisco Estuary (estuary) utilize EC as a primary simulation constituent, treating it as a conservative quantity. Such a modeling approach has likely been followed to exploit the wide availability of EC data for model calibration and validation, and to obviate the need to translate between EC and salinity in a domain characterized by multiple source waters with varying ionic make-ups. Arguably, this approach provides a reasonable trade-off between data translation error and model simulation error. In this paper, we critically evaluate this approach, employing an extensive salinity data set that includes measurements of EC and major ion concentrations in the estuary. We demonstrate and quantify EC deviation from steady-state, conservative mixing behavior; review the conservative mixing behavior of three bulk salinity measures (practical salinity, ionic strength, and limiting equivalent conductance); and evaluate their source-dependent correlations with EC in the estuary. We find limiting equivalent conductance—a value that assumes uninhibited mobility among individual ions in a water sample—to be an attractive alternative for salinity transport in the estuary. In addition to being a conservative quantity, it is consistently correlated with EC in the estuary’s dominant source waters, and thus addresses concerns related to data-translation error. We conclude this paper discussing pros and cons of adopting various salinity-transport model constituents.