Skip to main content
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 20, Issue 3, 2022

Issue cover
Cover Caption:Tule grows in the habitat surrounding the future location of the Lookout Slough Tidal Restoration Project. Image credit: Florence Low / California Department of Water Resources.

Research Article

I’m Not that Shallow – Different Zooplankton Abundance but Similar Community Composition Between Habitats in the San Francisco Estuary

Wetland restoration is a key management tool for increasing food availability for at-risk fishes in the San Francisco Estuary. To characterize the benefits of restoration sites, it is critical to quantify the abundance and composition of fish food resources in and near the wetlands. Characterization of zooplankton communities is considered particularly important, but accurate analysis of zooplankton samples is time-consuming and expensive. The recently established Fish Restoration Program (FRP) Monitoring Team assessed whether data from existing long-term monitoring surveys could be used to characterize shallow-water zooplankton communities prior to restoration. During the springs of 2017-2019, FRP collected zooplankton samples near the mouth of tidal wetland sites, or immediately outside future restoration sites, and compared them to concurrent samples collected in deep water by existing long-term monitoring surveys. We found very few differences in community composition between shallow and deep samples, though a few taxa were more abundant in shallow water. Seasonal and inter-annual differences in composition and abundance showed that restoration sites provide varying food resources over time. There was significantly higher total abundance of zooplankton in deep versus shallow water, which may be due to differences in zooplankton production, migration, or fish predation. There may also be inconsistencies in towing speed and gear type driving this result, rather than true habitat differences. This study indicates that monitoring of wetland restoration sites must rely on multiple years of data collected on the site, rather than relying on adjacent open-water sampling, and should include monitoring of epiphytic and epibenthic invertebrates as well as zooplankton.

Wakasagi in the San Francisco Bay–Delta Watershed: Comparative Trends in Distribution and Life-History Traits with Native Delta Smelt

Intentional introductions of non-native fishes can have severe consequences on native communities. Wakasagi (Hypomesus nipponensis, referred to as Japanese Pond Smelt) are native to Japan and were once separated from their non-native congener the endangered Delta Smelt (Hypomesus transpacificus) of the San Francisco Estuary (hereon ‘estuary’) of California (CA). Wakasagi were introduced into CA reservoirs in the 20th century as forage fish. Wakasagi have since expanded their distribution downstream to the estuary, but less is known about Wakasagi’s current distribution status and biology in the estuary, and negative influences on Delta Smelt. In this study, we took a comparative approach by synthesizing long-term field monitoring surveys, modeling environmental associations, and quantifying phenology, growth, and diets of Wakasagi and Delta Smelt to describe abundance and range, trends of co-occurrence, and shared ecological roles between smelt species. We found Wakasagi in greatest abundance in the upper watershed below source reservoirs and in the northern regions of the estuary with the most co-occurrence with Delta Smelt; however, their range extends to western regions of the estuary, and we found evidence of an established population that annually spawns and rears in the estuary. We found these smelt species have similar ecological roles demonstrated by overlaps in habitat use (e.g., an association with higher turbidities and higher outflow), phenology, growth, and diets. Despite similarities, earlier hatching and rearing of Wakasagi during cooler months and reduced growth during warmer drought years suggest this species is unlike typical non-natives (e.g., Centrarchids), and they exhibit a similar sensitivity to environmental variability as Delta Smelt. This sensitivity may be why Wakasagi abundance remains relatively low in the estuary.

  • 1 supplemental PDF

Estuarine Recruitment of Longfin Smelt (Spirinchus thaleichthys) North of the San Francisco Estuary

Longfin Smelt (Spirinchus thaleichthys) was an important forage fish in the San Francisco Estuary (SFE) but was listed as threatened under the California Endangered Species Act in 2009. This has inspired research within the SFE at the southern edge of their distribution. However, populations also exist in other estuaries along the coast, which are far less described despite their potential importance in a metapopulation. We surveyed Longfin Smelt populations along the northern California coast for larval recruitment. We conducted surveys in 2019 and 2020 to (1) identify estuaries north of SFE where spawning occurs, and (2) evaluate how habitat features (e.g., salinity, temperature, dissolved oxygen, turbidity) influenced Longfin Smelt larvae abundance. We detected larvae in four of 16 estuaries we surveyed, and all were large estuaries north of Cape Mendocino. No larvae were detected in eight coastal estuaries in closer proximity to the SFE. Larvae catch probability increased with turbidity and decreased with salinity with no significant influence of temperature and dissolved oxygen. In the wet winter of 2019, we observed lower densities of larvae in Humboldt Bay and the Eel River and detected no Longfin Smelt in the Klamath and Mad Rivers, while in the dry winter of 2020, we detected larvae in two additional estuaries. Elevated freshwater outflow in 2019 possibly increased transport rates to sea, resulting in observed low larval recruitment. Our results sugget that, although populations of Longfin Smelt exist in large estuaries north of Cape Mendocino, coastal estuaries in proximity to the SFE were either under sampled or are not permanently inhabited by Longfin Smelt. Longfin Smelt in the SFE may therefore lack resilience normally afforded by metapopulations. Increased monitoring over their coastal range under varying hydrologic conditions is needed to assess gene flow between populations.

  • 1 supplemental PDF

Habitat-Specific Foraging by Striped Bass (Morone saxatilis) in the San Francisco Estuary, California: Implications for Tidal Restoration

Non-native predatory fish strongly impact aquatic communities, and their impacts can be exacerbated by anthropogenic habitat alterations. Loss of natural habitat and restoration actions reversing habitat loss can modify relationships between non-native predators and prey. Predicting how these relationships will change is often difficult because insufficient information exists on the habitat-specific feeding ecology of non-native predators. To address this information gap, we examined diets of non-native Striped Bass (Morone saxatilis; 63 to 671 mm standard length; estimated age 1-5 yrs) in the San Francisco Estuary during spring and summer in three habitat types – marsh, shoal, and channel – with the marsh habitat type serving as a model for ongoing and future restoration. Based on a prey-specific index of relative importance, Striped Bass diets were dominated by macroinvertebrates in spring and summer (amphipods in spring, decapods and isopods in summer). In spring, diets were relatively consistent across habitats. In summer, marsh diets were dominated by sphaeromatid isopods and shoal/channel diets by idoteid amphipods and decapods. Striped Bass consumed a variety of native and non-native fishes, primarily Prickly Sculpin (Cottus asper) and Gobiidae. The highest importance of fish prey was in the marsh in spring (~40% prey weight), and fish prey comprised less than 25% prey weight in all other season/habitat combinations. Linear discriminant analyses suggested that marsh foraging was prevalent in Striped Bass collected in other habitats, mostly due to the predominance of marsh-associated invertebrates found in the stomachs of individual Striped Bass collected outside of the marsh. Striped Bass diets differ across habitats, with marsh foraging important to Striped Bass regardless of collection location. This information can be used to forecast the potential utilization of restored habitats by this non-native piscivore.

  • 1 supplemental PDF

A Framework for Evaluating the Effects of Reduced Spatial or Temporal Monitoring Effort

Monitoring in the San Francisco Estuary has fluctuated in sampling effort over time with changes to resources, objectives, and unforeseen events. I designed an approach to evaluate how reduced sampling would alter our ability to describe the status and trends of key species. This approach can evaluate the sensitivity of the estuary monitoring program to disruptions in sampling and whether sampling effort could be reduced without compromising the information provided by these surveys. I simulated reduced sampling on top of the historical data record (1985 – 2018) by selectively removing data and evaluating the impact on model inference. The same model structure is fit to the full dataset and several reduced datasets representing simulations of reduced sampling effort. Model predictions from reduced models are then compared to those from the full model to evaluate how reduced sampling may have affected our ability to detect key patterns in the data. In a case study, I applied this approach to Sacramento Splittail abundance trends from the Bay Study and the Suisun Marsh Fish Study otter trawls. Sampling reductions of 10 and 20% had fairly low impacts on the overlap of reduced model predictions with those from the full model. These results demonstrate the utility of my approach, but they are not generalizable beyond our ability to detect trends in Splittail abundance from Bay Study and Suisun Marsh Fish Study otter trawl data. A thorough analysis should run these simulations on multiple species and multiple parameters (e.g., abundance, distribution, length). By simulating sampling reductions on top of historical conditions, this approach could evaluate differential impacts in varying environmental or historical conditions (e.g., droughts, species declines, invasions). In addition, it can easily be extended to other functional groups (e.g., zooplankton, phytoplankton) as well as physical parameters (e.g., temperature, salinity, Secchi depth).