Marsh Sediment in Translation: A Review of Sediment Transport Across a Natural Tidal Salt Marsh in Northern San Francisco Bay

University of California, Davis (UC Davis) | March 15th, 2025

Deposition of inorganic sediment is essential for the sustainability of tidal salt marshes. Understanding variability in sediment sources and the processes of sediment de

Deposition of inorganic sediment is essential for the sustainability of tidal salt marshes. Understanding variability in sediment sources and the processes of sediment delivery to salt marshes are high priorities for decision-makers responsible for managing sediment and conserving and restoring marshes.

Mercury and Methylmercury in Fish and Water from the Sacramento-San Joaquin Delta: August 2016 – April 2017

San Francisco Estuary Institute (SFEI) | September 3rd, 2018

Monitoring of sport fish and water was conducted by the Delta Regional Monitoring Program (Delta RMP) from August 2016 to April 2017 to begin to address the highest prior

Monitoring of sport fish and water was conducted by the Delta Regional Monitoring Program (Delta RMP) from August 2016 to April 2017 to begin to address the highest priority information needs related to implementation of the Sacramento–San Joaquin Delta Estuary Total Maximum Daily Load (TMDL) for Methylmercury (Wood et al. 2010). Two species of sport fish, largemouth bass (Micropterus salmoides) and spotted bass (Micropterus punctulatus), were collected at six sampling locations in August and September 2016. The length-adjusted (350 mm) mean methylmercury (measured as total mercury, which is a routinely used proxy for methylmercury in predator fish) concentration in bass ranged from 0.15 mg/kg or parts per million (ppm) wet weight at Little Potato Slough to 0.61 ppm at the Sacramento River at Freeport. Water samples were collected on four occasions from August 2016 through April 2017. Concentrations of methylmercury in unfiltered water ranged from 0.021 to 0.22 ng/L or parts per trillion. Concentrations of total mercury in unfiltered water ranged from 0.91 to 13 ng/L. Over 99% of the lab results for this project met the requirements of the Delta RMP Quality Assurance Program Plan, and all data were reportable. This data report presents the methods and results for the first year of monitoring. Historic data from the same or nearby monitoring stations from 1998 to 2011 are also presented to provide context. Monitoring results for both sport fish and water were generally comparable to historic observations. For the next several years, annual monitoring of sport fish will be conducted to firmly establish baseline concentrations and interannual variation in support of monitoring of long-term trends as an essential performance measure for the TMDL. Monitoring of water will solidify the linkage analysis (the quantitative relationship between methylmercury in water and methylmercury in sport fish) in the TMDL. Water monitoring will also provide data that will be useful in verifying patterns and trends predicted by numerical models of mercury transport and cycling being developed for the Delta and Yolo Bypass by the California Department of Water Resources (DWR).

Meta-analysis reveals negative yet variable effects of ocean acidification on marine organisms: Biological responses to ocean acidification

Ecology Letters (Wiley) | August 16th, 2010

Ocean acidification is a pervasive stressor that could affect many marine organisms and cause profound ecological shifts. A variety of biological responses to ocean acid

Ocean acidification is a pervasive stressor that could affect many marine organisms and cause profound ecological shifts. A variety of biological responses to ocean acidification have been measured across a range of taxa, but this information exists as case studies and has not been synthesized into meaningful comparisons amongst response variables and functional groups. We used meta-analytic techniques to explore the biological responses to ocean acidification, and found negative effects on survival, calcification, growth and reproduction. However, there was significant variation in the sensitivity of marine organisms. Calcifying organisms generally exhibited larger negative responses than non-calcifying organisms across numerous response variables, with the exception ofcrustaceans, which calcify but were not negatively affected. Calcification responses varied significantly amongst organisms using different mineral forms of calcium carbonate.Organisms using one of the more soluble forms of calcium carbonate (high-magnesium calcite) can be more resilient to ocean acidification than less soluble forms (calcite and aragonite). Additionally, there was variation in the sensitivities of different developmental stages, but this variation was dependent on the taxonomic group. Our analyses suggest that the biological effects of ocean acidification are generally large and negative, but the variation in sensitivity amongst organisms has important implications for ecosystem responses.

Methodology for Flow and Salinity Estimates in the Sacramento-San Joaquin Delta and Suisun Marsh

California Department of Water Resources (DWR) | June 15th, 2022

This is the 43rd annual progress report of the California Department of Water Resources’ San Francisco Bay-Delta Evaluation Program, which is carried out by the Delta M

This is the 43rd annual progress report of the California Department of Water Resources’ San Francisco Bay-Delta Evaluation Program, which is carried out by the Delta Modeling Section. This report is submitted annually to the State Water Resources Control Board pursuant to its Water Right Decision D-1485, Term 9, which is still active pursuant to its Water Right Decision D-1641, Term 8. This report documents progress in the development and enhancement of computer models for the Delta Modeling Section of the Bay-Delta Office. It also reports the latest findings of studies conducted as part of the program. This report was compiled under the direction of Nicky Sandhu, Program Manager for the Bay-Delta Evaluation Program.

Methodology for Flow and Salinity Estimates in the Sacramento-San Joaquin Delta and Suisun Marsh

California Department of Water Resources (DWR) | December 1st, 2019

Various water resource management actions have been planned to protect and restore salmon populations for a healthy Sacramento-San Joaquin Delta (Delta) ecosystem. Curren

Various water resource management actions have been planned to protect and restore salmon populations for a healthy Sacramento-San Joaquin Delta (Delta) ecosystem. Currently, evaluating the effectiveness of these actions relies on field studies and/or expert opinion. Field studies can be costly and may not provide a comprehensive assessment for a range of applications because of limited study areas, durations, and river conditions. Expert opinion, although valuable, may under- or over-emphasize the importance of certain project components.  To supplement field studies and provide a quantitative assessment tool, the California Department of Water Resources (DWR), in collaboration with the United States Geological Survey (USGS), developed an ecological modeling tool, ECO-PTM. ECO-PTM is an individual-based juvenile salmon migration model that is based on a random-walk particle-tracking method with fish-like behaviors attached to the particles. The behavioral parameters are estimated from acoustic telemetry tag data of juvenile late-fall Chinook salmon (Tag Data) from various field studies (Perry et al. 2018). A stochastic optimization tool, Particle Swarm Optimization, is used to calibrate the swimming behavior parameters. ECO-PTM can simulate juvenile salmonid migration timing, routing, and survival.  This chapter describes ECO-PTM and its behavioral modules, and the model performance and applications to assist water resource management planning, assessment, and decision-making related to juvenile salmonid survival outcomes. 

Microparticles, Microplastics, and PAHs in Bivalves in San Francisco Bay

San Francisco Estuary Institute (SFEI) | November 15th, 2019

Microplastics in Lake Mead National Recreation Area, USA: Occurrence and biological uptake

PLOS | May 4th, 2020

Microplastics are an environmental contaminant of growing concern, but there is a lack of information about microplastic distribution, persistence, availability, and bio

Microplastics are an environmental contaminant of growing concern, but there is a lack of information about microplastic distribution, persistence, availability, and biological uptake in freshwater systems. This is especially true for large river systems like the Colorado River that spans multiple states through mostly rural and agricultural land use. This study characterized the quantity and morphology of microplastics in different environmental compartments in two large reservoirs along the Colorado River: Lakes Mead and Mohave, within Lake Mead National Recreation Area. To assess microplastic occurrence, surface water and surficial sediment were sampled at a total of nine locations. Sampling locations targeted different sub-basins with varying levels of anthropogenic impact. Las Vegas Wash, a tributary which delivers treated wastewater to Lake Mead, was also sampled. A sediment core (33 cm long, representing approximately 19 years) was extracted from Las Vegas Bay to assess changes in microplastic deposition over time. Striped bass (Morone saxatilis), common carp (Cyprinus carpio), quagga mussels (Dreissena bugensis), and Asian clams (Corbicula fluminea) were sampled at a subset of locations to assess biological uptake of microplastics. Microplastic concentrations were 0.44–9.7 particles/cubic meter at the water surface and 87.5–1,010 particles/kilogram dry weight (kg dw) at the sediment surface. Sediment core concentrations were 220–2,040 particles/kg dw, with no clear increasing or decreasing trend over time. Shellfish microplastic concentrations ranged from 2.7–105 particles/organism, and fish concentrations ranged from 0–19 particles/organism. Fibers were the most abundant particle type found in all sample types. Although sample numbers are small, microplastic concentrations appear to be higher in areas of greater anthropogenic impact. Results from this study improve our understanding of the occurrence and biological uptake of microplastics in Lake Mead National Recreation Area, and help fill existing knowledge gaps on microplastics in freshwater environments in the southwestern U.S.

Missing the Boat on Freshwater Fish Conservation in California

Conservation Letters (Society for Conservation Biology) | March 30th, 2016

Population growth and increasing water‐use pressures threaten California's freshwater ecosystems and have led many native fishes to the brink of extinction. To guide fi

Population growth and increasing water‐use pressures threaten California's freshwater ecosystems and have led many native fishes to the brink of extinction. To guide fish conservation efforts, we provide the first systematic prioritization of river catchments and identify those that disproportionately contribute to fish taxonomic diversity. Using high‐resolution range maps of exceptional quality, we also assess the representation of fish taxa within the state's protected areas and examine the concordance of high‐priority catchments with existing reserves and among distinct taxonomic groups. Although most of the state's native fishes are found within protected areas, only a small proportion of their ranges are represented. Few high‐priority catchments occur within protected areas, suggesting that fish conservation will require active management and targeted river restoration outside of reserves. These results provide the foundation for systematic freshwater conservation planning in California and for prioritizing where limited resources are allocated for fish recovery and protection.

Modeling Functional Flows in California’s Rivers

Frontiers in Environmental Science (Frontiers) | March 11th, 2022

Modeling the dispersal of the San Francisco Bay plume over the Northern and central California shelf

Estuarine, Coastal and Shelf Science (Elsevier) | April 19th, 2023

High-resolution simulations by the Regional Ocean Modeling System (ROMS) were used to investigate the dispersal of the San Francisco Bay (SFB) plume over the northern-cen

High-resolution simulations by the Regional Ocean Modeling System (ROMS) were used to investigate the dispersal of the San Francisco Bay (SFB) plume over the northern-central California continental shelf during the period of 2011 to 2012. The modeled bulk dynamics of surface currents and state variables showed many similarities to corresponding observations. After entering the Pacific Ocean through the Golden Gate, the SFB plume is dispersed across the shelf via three pathways: (i) along the southern coast towards Monterey Bay, (ii) along the northern coast towards Point Arena, and (iii) an offshore pathway restricted within the shelf break. On the two-year mean timescale, the along-shore zone of impact of the northward-dispersed plume is about 1.5 times longer than that of the southern branch. Due to the opposite surface Ekman transports induced by the northerly or southerly winds, the southern plume branch occupies a broader cross-shore extent, roughly twice as wide as the northern branch which extends roughly two times deeper due to coastal downwelling. Besides these mean characteristics, the SFB plume dispersal also shows considerable temporal variability in response to various forcings, with wind and surface-current forcing most strongly related to the dispersing direction. Applying constituent-oriented age theory, we determine that it can be as long as 50 days since the SFB plume was last in contact with SFB before being flushed away from the Gulf of the Farallones. This study sheds light on the transport and fate of SFB plume and its impact zone with implications for California’s marine ecosystems.