San Francisco Estuary and Watershed Science

Tidal marsh restoration is an important management issue in the San Francisco Estuary (estuary). Restoration of large areas of tidal marsh is ongoing or planned in the lower estuary (up to 6,000 ha, Callaway et al. 2011). Large areas are proposed for restoration in the upper estuary under the Endangered Species Act biological opinions (3,237 ha) and the Bay Delta Conservation Plan (26,305 ha). In the lower estuary, tidal marsh has proven its value to a wide array of species that live within it (Palaima 2012). In the Sacramento–San Joaquin Delta (Delta), one important function ascribed to restoration of freshwater tidal marshes is that they make large contributions to the food web of fish in open waters (BDCP 2013). The Ecosystem Restoration Program ascribed a suite of ecological functions to tidal marsh restoration, including habitat and food web benefits to native fish (CDFW 2010). This background was the basis for a symposium, Tidal Marshes and Native Fishes in the Delta: Will Restoration Make a Difference? held at the University of California, Davis, on June 10, 2013. This paper summarizes conclusions the authors drew from the symposium.

Steelhead trout (Oncorhynchus mykiss) historically occurred in all major watersheds along the west coast of the United States. They can be a vital part of a healthy riverine ecosystem, are highly valued for fishing, and have been greatly affected by human activities. Given these traits, and that the San Joaquin River in the Central Valley of California is under consideration for steelhead reintroduction, emphasis has recently been placed on conservation efforts to reintroduce steelhead into streams in which they were once native. There are many issues to consider when deciding how, where, and in what manner to reintroduce steelhead, including genetic considerations. One primary factor is determining the source population for reintroduction. In this paper, we consider the many important genetic aspects to consider when determining the source for steelhead reintroduction, and outline the genetic data needs when determining sources for reintroduction. We discuss the lessons learned from previous reintroductions in relation to a reintroduction scenario in the San Joaquin River, and recommend potential source populations.

Sea level rise, large-scale flooding, and new conveyance arrangements for water exports may increase future water salinity for local agricultural production in California’s Sacramento–San Joaquin Delta. Increasing salinity in crop root zones often decreases crop yields and crop revenues. Salinity effects are nonlinear, and vary with crop choice and other factors including drainage and residence time of irrigation water. Here, we explore changes in agricultural production in the Delta under various combinations of water management, large-scale flooding, and future sea level rise. Water management alternatives include through-Delta water exports (current conditions), dual conveyance (through-Delta and a 6,700 Mm³ yr^‑1 [or 7500 cfs] capacity peripheral canal or tunnel) and the flooding of five western islands with and without peripheral exports. We employ results from previous hydrodynamic simulations of likely changes in salinity for irrigation water at points in the Delta. We connect these irrigation water salinity values into a detailed agro-economic model of Delta agriculture to estimate local crop yield and farm revenue losses. Previous hydrodynamic modeling work shows that sea level rise is likely to increase salinity from 4% to 130% in this century, depending on the increase in sea level and location. Changes in water management under dual conveyance increase salinity mostly in the western Delta, and to a lesser extent in the north, where current salinity levels are now quite low. Because locations likely to experience the largest salinity increases already have a lower-value crop mix, the worst-case losses are less than 1% of total Delta crop revenues. This result also holds for salinity increases from permanent flooding of western islands that serve as a salinity barrier. Our results suggest that salinity increases could have much smaller economic effects on Delta farming than other likely changes in the Delta such as retirement of agricultural lands after large-scale flooding and habitat development. Integrating hydrodynamic, water salinity, and economic models can provide insights into controversial management issues.

The freshwater Siberian prawn, Exopalaemon modestus (Heller 1862, Crustacea: Decapoda: Palaemonidae), was likely introduced into the San Francisco Estuary in the late 1990s. Since the initial collection in 2000, E. modestus spread rapidly throughout the estuary and into upstream areas, and is now the most common caridean shrimp in the upper estuary, including the Sacramento–San Joaquin Delta. We summarized data collected from 2000 to 2011 by several long-term monitoring projects, special studies, and the public concerning E. modestus in California. Although some specific ecological effects of this introduced species have been documented, broader effects are largely unknown. E. modestus is likely to expand its distribution within the estuary and watershed and become established in other freshwater areas of California.

Tidal marsh wetlands provide important foraging habitat for a variety of estuarine fishes. Prey organisms include benthic–epibenthic macroinvertebrates, neustonic arthropods, and zooplankton. Little is known about the abundance and distribution of interior marsh macroinvertebrate communities in the San Francisco Estuary (estuary). We describe seasonal, regional, and site variation in the composition and abundance of neuston and benthic–epibenthic macroinvertebrates that inhabit tidal marsh channels, and relate these patterns to environmental conditions. We also describe spatial and temporal variation in diets of marsh-associated inland silverside, yellowfin goby, and western mosquitofish. Fish and invertebrates were sampled quarterly from October 2003 to June 2005 at six marsh sites located in three river systems of the northern estuary: Petaluma River, Napa River, and  the west Delta. Benthic/epibenthic macroinvertebrates and neuston responded to environmental variables related to seasonal changes (i.e., temperature, salinity), as well as those related to marsh structure (i.e., vegetation, channel edge). The greatest variation in abundance occurred seasonally for neuston and spatially for benthic–epibenthic organisms, suggesting that each community responds to different environmental drivers. Benthic/epibenthic invertebrate abundance and diversity was lowest in the west Delta, and increased with increasing salinity. Insect abundance increased during the spring and summer, while Collembolan (springtail) abundance increased during the winter. Benthic/epibenthic macroinvertebrates dominated fish diets, supplemented by insects, with zooplankton playing a minor role. Diet compositions of the three fish species overlapped considerably, with strong selection indicated for epibenthic crustaceans—a surprising result given the typical classification of Menidia beryllina as a planktivore, Acanthogobius flavimanus as a benthic predator, and Gambusia affinis as a larvivorous surface-feeder. Fish diets were influenced by position along the estuarine gradient and season. Overall, our data show that local-scale site effects and marsh position within the estuary influence invertebrate community composition and abundance. Additionally, we show that restoring marsh ecosystems can subsidize fishes similarly to reference marshes. We, thus, recommend that managers focus on the ability of restoring marshes to produce food subsidies for target species when planning and designing tidal marsh restoration projects, especially those targeted for food web support.