San Francisco Estuary and Watershed Science

Variation in Juvenile Salmon Growth Opportunities Across a Shifting Habitat Mosaic

Coleman et al. found that juvenile Chinook Salmon grew faster in the Delta in some years (2016), but slower in the Delta during drought conditions (2014 to 2015). Habitat that featured faster growth rates varied within and among years, suggesting the importance of maintaining a habitat mosaic for juvenile salmonids, particularly in a dynamic environment such as the California Central Valley.

Relative Bias in Catch Among Long-Term Fish Monitoring Surveys Within the San Francisco Estuary

Huntsman et al. assessed relative catchability differences among four long-term fish monitoring surveys from the San Francisco Estuary. Their results demonstrate that catchability is a source of bias among monitoring efforts within the San Francisco Estuary, and assuming equal catchability among surveys, species, and size classes could result in significant bias when describing spatio-temporal patterns in catch if ignored.

Investigation of Molecular Pathogen Screening Assays for Use in Delta Smelt

Gille et al. conducted a pilot study that applied molecular assays originally developed in salmonids to assess the presence of a wide variety of pathogens in the gill tissue of cultured and wild Delta Smelt—as well as cultured fish—deployed in enclosures in the estuary. Although disease is not an overt cause of population decline of Delta Smelt in the San Francisco Estuary, comprehensive pathogen presence and prevalence data are lacking, and unintended transmission of pathogens can have devastating effects on populations already at-risk or on the natural ecosystem at large. Their results corroborate previous work that cultured Delta Smelt do not appear to present a high risk for pathogen transmission during population supplementation or reintroduction.

Multi-Biomarker Analysis for Identifying Organic Matter Sources in Small Mountainous River Watersheds: A Case Study of the Yuba River Watershed

Pondell and Canuel's study focused on identifying the composition of watershed-derived organic matter (OM). To better understand inputs to inland waters and improve distinguish between terrigenous and aquatic sources in downstream systems, such as estuaries and coasts, they surveyed OM sources from the Yuba River watershed in northern California to identify specific biomarkers that represent aquatic and terrigenous OM sources. Results demonstrate the utility of multi-biomarker studies for distinguishing between OM from different sources and land uses, offering new insights for biogeochemical studies in aquatic systems.

Volume 7, Issue 2, 2009

Research Article

Nearshore Areas Used by Fry Chinook Salmon, Oncorhynchus tshawytscha, in the Northwestern Sacramento–San Joaquin Delta, California

We reported the geographic distribution and the densities and catch rates of fry Chinook salmon, Oncorhynchus tshawytscha, found in different substrata and nearshore zones in the northwestern Sacramento-San Joaquin Delta of the San Francisco Estuary, California, USA. Nearshore zones in the fresh-water, tidally influenced northwest delta were dominated by riprap, and contained sparse sections of tule beds, beaches, and riparian zones. A total of six beach seine sites and eight electrofish sites were sampled during winter 2001 along the Sacramento River, Steamboat Slough, Miner Slough, Prospect Island Marsh, Prospect Slough, and Liberty Island Marsh. Overall, fry densities were higher on the Sacramento River and Steamboat Slough and lower in Liberty and Prospect Island marshes. Chinook salmon fry were significantly larger in the Sacramento River than in Steamboat Slough during March. Highest densities of Chinook salmon fry were observed in shallow beaches than in riprap nearshore zones. Fry densities also increased with Secchi depth and richness of non-native predators, suggesting increased predation risk by opportunistic predators. Shallow nearshore environments in conveyance channels, such as Steamboat Slough and the Sacramento River, seem important for Chinook salmon fry rearing. Conversely, riprap in these channels could reduce fry rearing habitat. Although fry catch rates by electrofishing did not differ greatly among riparian, riprap, beach and tule nearshore zones, they were on average about one-third higher in beaches. Evaluating potential impacts of habitat quality on growth and survival of fry seems key to further assess and monitor restoration efforts in the delta.

Three-dimensional Modeling of Tidal Hydrodynamics in the San Francisco Estuary

Simulations of circulation in the San Francisco Estuary were performed with the three-dimensional TRIM3D hydrodynamic model using a generic length scale turbulence closure. The model was calibrated to reproduce observed tidal elevations, tidal currents, and salinity observations in the San Francisco Estuary using data collected during 1996-1998, a period of high and variable freshwater flow. It was then validated for 1994-1995, with emphasis on spring of 1994, a period of intensive data collection in the northern estuary. The model predicts tidal elevations and tidal currents accurately, and realistically predicts salinity at both the seasonal and tidal time scales. The model represents salt intrusion into the estuary accurately, and therefore accurately represents the salt balance. The model’s accuracy is adequate for its intended purposes of predicting salinity, analyzing gravitational circulation, and driving a particle-tracking model. Two applications were used to demonstrate the utility of the model. We estimated the components of the longitudinal salt flux and examined their dependence on flow conditions, and compared predicted salt intrusion with estimates from two empirical models.

2 supplemental PDFs

Salinity Trends, Variability, and Control in the Northern Reach of the San Francisco Estuary

The State and federal water projects decoupled long-term trends in annual mean outflow and salinity from long-term trends in precipitation. The water projects also dampen seasonal and annual outflow and salinity variability. Despite this, both seasonal and annual timescale outflow and salinity are generally more variable in the water project era concordant with watershed precipitation. We re-constructed monthly time series of precipitation, outflow, and salinity for the northern reach. These include salinity at Port Chicago (since 1947), Beldons Landing (since 1929), and Collinsville (since 1921), Delta outflow (since 1929), and a San Francisco Estuary watershed precipitation index (since 1921). We decomposed data into seasonal, decadal, and trend components to clarify the superposition of variability drivers. With the longest time series over 1000 months, these are the longest data records in the estuary save for Golden Gate tide. We used the precipitation index to compare trends and variability in climate forcing to outflow and salinity trends before and after construction of the water projects and the Suisun Marsh Salinity Control Gate. We test the widely held conceptual model that water project reservoir and Delta export operations reduce seasonal and annual outflow variability. We found that the water projects influence the trend of the annual and some monthly means in outflow and salinity, but exert far less influence on variability. We suggest that climate is the primary variability driver at timescales between one-month and ~20 years. We underscore the understanding that identifying trends and mechanisms requires data sets that are longer than the timescale of the lowest frequency forcing mechanism.