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At least 73 records · Page 4Linked to original sources
USGS2022

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.

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USGS2023

Ecology and ecosystem impacts of submerged and floating aquatic vegetation in the Sacramento-San Joaquin Delta

Substantial increases in non-native aquatic vegetation have occurred in the upper San Francisco Estuary over the last 2 decades, largely from the explosive growth of a few submerged and floating aquatic plant species. Some of these species act as ecosystem engineers by creating conditions that favor their further growth and expansion as well as by modifying habitat for other organisms. Over the last decade, numerous studies have investigated patterns of expansion and turn-over of aquatic vegetation species; effects of vegetation on ecosystem health, water quality, and habitat; and effects of particular species or communities on physical processes such as carbon and sediment dynamics. Taking a synthetic approach to evaluate what has been learned over the last few years has shed light on just how significant aquatic plant species and communities are to ecosystems in the Sacramento-San Joaquin Delta. Aquatic vegetation affects every aspect of the physical and biotic environment, acting as ecosystem engineers on the landscape. Furthermore, their effects are constantly changing across space and time, leaving many unanswered questions about the full effects of aquatic vegetation on Delta ecosystems and what future effects may result, as species shift in distribution and new species are introduced. Remaining knowledge gaps underlie our understanding of aquatic macrophyte effects on Delta ecosystems, including their roles and relationships with respect to nutrients and nutrient cycling, evapotranspiration and water budgets, carbon and sediment, and emerging effects on fish species and their habitats. This paper explores our current understanding of submerged and floating aquatic vegetation (SAV and FAV) ecology with respect to major aquatic plant communities, observed patterns of change, interactions between aquatic vegetation and the physical environment, and how these factors affect ecosystem services and disservices within the upper San Francisco Estuary.

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USGS2023

Carbon sequestration and subsidence reversal in the Sacramento-San Joaquin Delta and Suisun Bay: Management opportunities for climate mitigation and adaptation

The aquatic landscapes of the Sacramento–San Joaquin Delta (hereafter, the Delta) and Suisun Bay represent both a significant past and future soil carbon stock. Historical alterations of hydrologic flows have led to depletion of soil carbon stocks via emissions of carbon dioxide (CO2), and loss of elevation as a result of subsidence. Optimizing ecosystem hydrology in the Delta and Suisun Bay could both reduce and reverse subsidence while also providing significant opportunities for climate mitigation and adaptation. Emissions of greenhouse gases (GHGs)—notably CO2, methane (CH4 ), and nitrous oxide (N2O)—contribute to global warming at different rates and intensities, requiring GHG accounting and modeling to assess the relative benefits of management options. Decades of data collection, model building, and map development suggest that past and current management actions have both caused—and can mitigate—losses of soil carbon. We review here the magnitude of potential GHG offsets, management options that may be achievable, and trade-offs of carbon storage under different land management. Using a land-use/land-cover framework to assess these management options, we describe the potential of three interventions (impoundment to reverse subsidence, agricultural management, and tidal reintroduction and/or maintained connectivity), both in acreage and radiative balance to clarify their relative influence on the region’s GHG balance today and in relation to its millennial history. From floodplains to farming to floating aquatic vegetation, we find specific scalable strategies to manage hydrology that can alter regional GHG balance. Preservation of soil carbon stocks and restoration of net atmospheric CO2 fluxes into soils are the primary route to net negative emissions in the Delta and Suisun Bay, with CH4 emission management occurring in a supporting role. Over a 40-year horizon of climate-mitigation markets, the resilience of different aquatic habitats introduces the most uncertainty, from expected and unexpected hydrologic changes associated with land, ocean, and operational water flows.

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USGS2023

What controls suspended-sediment concentration and export in flooded agricultural tracts in the Sacramento-San Joaquin Delta?

We investigated wind-wave and suspended-sediment dynamics in Little Holland Tract and Liberty Island, two subsided former agricultural tracts in the Cache Slough complex in the northern Sacramento-San Joaquin Delta which were restored to tidal shallows to improve habitat. Turbidity, and thus suspended-sediment concentration (SSC), is important to habitat quality because some species of native fishes, including the Delta Smelt, are found preferentially in more turbid waters. Data from October 2015 to August 2016 show that average SSC was greater within Little Holland Tract than in the primary breach that connects the basin to surrounding channels: approximately twice as great at a shallower station farther from the breach and 15% greater at a deeper station closer to the breach. Suspended-sediment concentration within Little Holland Tract was directly related to wave shear stress and inversely related to water depth, based on linear regression. We used measurements of suspended-sediment flux (SSF) through the largest levee breaches to assess whether the enhanced SSC within Little Holland Tract is exported to surrounding waters, thus potentially increasing turbidity over a wider region. Cumulatively, sediment is exported through the Little Holland Tract breaches in winter and imported in summer, consistent with regional patterns in sediment flux, indicating that wind-wave re-suspension within the basin does not control sediment flux from Little Holland Tract on seasonal time-scales. Some sediment was exported during wind-wave events, and results show that sediment export is greater when primary breaches are located downwind of the basin rather than upwind.

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USGS2023

Habitat use by breeding waterbirds in relation to tidal marsh restoration in the San Francisco Bay estuary

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.

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USGS2023

A simple approach to modeling light attenuation in the Sacramento-San Joaquin Delta using commonly available data

The diffuse attenuation coefficient of photosynthetically active radiation (KdPAR) is commonly used to predict light attenuation in aquatic productivity models, but obtaining measurements of PAR to compute KdPAR is difficult. In situ calculations of KdPAR require multiple measurements of PAR through the water column, and these measurements are infeasible for real-time recording. Instead, predictive models using surface-water measurements may be used. Traditional KdPAR models are based on open-ocean habitats and rely on chlorophyll—as a proxy measurement for phytoplankton abundance—as the main predictive parameter. However, elevated suspended sediments and dissolved organic materials may also affect KdPAR values of inland water bodies and estuaries. In this study, we leverage KdPAR calculations derived from in situ light measurements collected along with surface-water-quality parameters across the Sacramento-San Joaquin River Delta in California, USA (the Delta). Sampling occurred between January of 2013 and May of 2014. We also explored regional and seasonal effects, but these did not clearly affect the model. Ultimately, the best-performing model included surface-level turbidity only (R2 = 0.91). The simplicity of the model facilitates use of KdPAR estimates for a variety of purposes throughout the Delta, including euphotic depth calculations, and as inputs to primary-productivity and habitat-suitability models. We demonstrate the model’s usability with two open-sources data sets (one spatially dense, and one temporally dense), and estimate KdPAR, euphotic depth, and primary productivity within the Delta. We provide calculations for each estimation, allowing users to easily adopt these models and apply them to their own data or with open-sourced data, which are abundant.

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USGS2024

The anatomy of a drought in the upper San Francisco Estuary: Water quality and lower-trophic responses to multi-year droughts

Multi-year droughts are important and impactful features of California’s Mediterranean climate and can fundamentally affect the water quality and the ecosystem response of the San Francisco Estuary (Estuary) and the Sacramento-San Joaquin Delta (Delta). This study assesses data collected by long-term monitoring programs over the past 46 years (1975-2021) to evaluate how water quality in the Estuary changes during multi-year droughts. We found that multi-year droughts alter multiple physical and chemical parameters in the Estuary, increasing water temperature, salinity, water clarity, and nutrient levels. This trend was consistent across regions and seasons, with few exceptions. Increases in these parameters during droughts are likely caused by reduced Delta inflows that intensified in each successive dry year because of reduced precipitation and reservoir releases. Droughts did not substantially effect on tidal velocities within the Estuary, which remained mostly consistent across wet and dry periods. Trends in chlorophyll concentrations during droughts were more nuanced with higher concentrations occurring in the South-Central Delta region and during the winter and spring. Together, these results paint a picture of drought in the Estuary as warm, clear, high in nutrients, with patchy phytoplankton blooms (as indexed by chlorophyll), all of which have implications for higher trophic levels. Considering that droughts are expected to increase in frequency and intensity in California with climate change, it is imperative to understand the effects of multi-year droughts on the water quality conditions of the Estuary when making water management decisions.

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USGS2024

Delta blue(green)s: The effect of drought and drought-management actions on microcystis in the Sacramento–San Joaquin Delta

Cyanobacterial phytoplankton blooms are more prevalent in the freshwater Sacramento-San Joaquin Delta (Delta) since the late 1990s, including blooms driven by overgrowths of potentially toxigenic organisms of the genus Microcystis . Data from 2014 to 2021 were used to show how flow dynamics, water temperature, and water clarity drive occurrence of Microcystis . We used a Microcystis bloom in the central Delta from 2021 as a case study for how novel monitoring tools can track blooms in real-time and be used post hoc to evaluate the effects of management actions. Microcystis was detected throughout the Delta in all but the highest-flow years, and bloom incidence and severity increased during drier years. In the South Delta, Franks Tract, lower San Joaquin River, and Old River regions, where blooms are most prevalent, higher water temperatures and clarities combined with lower exports from state and federal water projects were the best explanatory factors for the occurrence of Microcystis blooms. Nutrient concentrations were lower in summer than in winter, but only became limiting at high phytoplankton concentrations. We used satellite data and in situ continuous monitoring of flow, phytoplankton communities, and water quality to track hydro-biogeochemical conditions during the 2021 case study Microcystis bloom in the Central Delta. We did not find evidence that changes to Delta outflow regulatory standards contributed to this bloom, but changes in flow caused by a salinity barrier placed in west False River may have exacerbated the bloom. The frequency and severity of droughts are expected to increase in the future as a result of climate change, and our study demonstrates how continued monitoring of cyanotoxins, water quality, and phytoplankton communities could help improve management of cyanobacterial blooms in the Delta and other estuaries.

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USGS2024

Climate change scenarios for air and water temperatures in the upper San Francisco Estuary: Implications for thermal regimes and Delta Smelt

Climate projections and their effects in the San Francisco Estuary have been evaluated as part of the US Geological Survey’s CASCaDE2 project. Understanding the ecological effects of climate change can help manage and maintain the ecological health and productivity of the San Francisco Estuary. In this study, we assessed downscaled air temperature data from 10 global climate models (GCMs) under two representative concentration pathway (RCP) trajectories for greenhouse gas concentrations for three regions of the San Francisco Estuary: Sacramento–San Joaquin Delta, Suisun and Grizzly bays, and Suisun Marsh. We also used previously derived regression models to estimate future water temperatures at 16 locations in the upper San Francisco Estuary. We used a thermal regime approach to summarize water temperature projections to investigate changes to the thermal regime of the upper San Francisco Estuary, and used the Delta Smelt (Hypomesus transpacificus) to demonstrate the effects that a warming climate may have on the habitat needs of this fish species. Our results suggested there were no major differences in the extent of air-temperature warming among the three regions. Annual average air temperatures were projected to increase approximately 2.0 °C and 4.7 °C by the end of the century for the low and high RCP scenarios, respectively. We found timing, frequency, and magnitude metrics varied by period and RCP scenario, while duration and variability metrics varied by space for water-temperature thermal regimes. For example, the spawning window for Delta Smelt (thermal-regime duration metric) is projected to expand in the future, with spawning starting earlier for both RCP scenarios for most sites. Although our thermal-regime analysis focused on the life history of Delta Smelt, similar approaches could be used to assess climate-change threats to a wide array of native and invasive terrestrial and aquatic species found in San Francisco Estuary.

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USGS2024

Managed wetlands for climate action: Potential greenhouse gas and subsidence mitigation in the Sacramento-San Joaquin Delta

In the Sacramento–San Joaquin Delta (Delta), widespread drainage of historical wetlands has led to extensive subsidence and peat carbon losses, as well as high ongoing greenhouse gas (GHG) emissions. Large-scale wetland restoration and conversion to rice fields has the potential to mitigate these effects while conferring flood protection and creating habitat for wetland species. To explore the scale of these potential benefits, this study evaluated the effects of seven Delta-wide land-use scenarios on carbon stocks, land-surface elevation, GHG emissions, and habitat. Peat mapping and data from peat cores indicate that soil carbon stocks have decreased between the early 1800s and 2010s from 288 ± 15 to 145 ± 14 million metric tons (Mt) of carbon (C). If existing land uses continue, the Delta could lose an additional 8.3 Mt C during the coming 40 years, equal to average GHG emissions of 1.2 Mt CO2 equivalents (CO2e) yr-1. Future restoration and rice-farming scenarios indicate that wetland restoration could theoretically halt GHG emissions, converting the Delta from a large GHG source to a weak net source or sink. Across three future scenarios based on existing restoration targets, wetland creation and conversion to rice fields reduced GHG emissions by 0.39 to 0.67 Mt CO2e yr-1, with per-area benefits of 16 to 28 t CO2e per hectare (ha) yr-1. Differences among scenarios in extents of wetland types influenced their relative benefits for different management goals. Tidal restoration and conversion to rice fields enhanced habitat benefits and offered a source of agricultural income, but with reduced GHG mitigation compared with conversion to peat-building wetlands. This highlights the importance of clear objectives when developing land-use plans. A strategic land-management portfolio that includes rice fields and both impounded and tidal wetlands could be designed to provide GHG and subsidence mitigation while offering a diverse suite of benefits for ecosystems and people.

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USGS2024

Surveying waterfowl broods in wetlands using aerial drones

Effective waterfowl management relies on the collection of relevant demographic data to inform land management decisions; however, some types of data are difficult to obtain. For waterfowl, brood surveys are difficult to conduct because wetland habitats often obscure ducklings from being visually assessed. Here, we used Unoccupied Aerial Systems (UAS) to assess what wetland habitat characteristics influenced brood abundance in Suisun Marsh, California, USA. Using a thermal imaging camera, we surveyed 17 wetland units encompassing 332 ha of flooded area on seven waterfowl hunting clubs during the waterfowl breeding season. Additionally, using a combination of multispectral imagery collected from the UAS flights and LiDAR data from the previous year, we mapped habitat composition within each unit to relate to brood observation counts. From June 3-7, 2019, we identified 113 individual broods comprised of 827 ducklings. We found a positive relationship between the number of broods observed and the proportion of the unit that was flooded. We also found a positive relationship between the number of broods observed and the area of effective habitat, a metric of flooded habitat within a specific distance of flooded vegetation. Brood surveys using UAS could complement the traditional Breeding Population Survey and provide local managers with fine-scale and timely information regarding shifts in brood abundance in the region.

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USGS2024

Bird habitat value and management priorities of the California Winter Rice Habitat Incentive Program

Flooding rice ( Oryza sativa ) agricultural fields during winter to facilitate rice straw decomposition has mitigated the loss of some of the natural wetlands in California’s Central Valley. We conducted bird surveys in 253 rice checks (2,158 ha) within 177 rice fields in the Sacramento Valley during the fall and winter of 2021-2022 and 2022-2023 to evaluate factors influencing bird use of winter-flooded, post-harvest rice fields enrolled in the California Winter Rice Habitat Incentive Program. We counted 143,932 birds from 57 species, including dabbling ducks (86.4%), geese (8.0%), shorebirds (0.9%), wading birds (0.7%), and other birds (4.0%). Extrapolating from the lowest densities observed in rice fields during the 70-day mandatory flooding period, we estimated that properties enrolled in this public-private partnership provided habitat for at least 271,312 birds day-1 (16,248 ha; 2021-2022) and 147,315 birds day-1 (8,448 ha; 2022-2023), totaling >10 million bird-use-days each winter. Water depth had the greatest influence on bird abundance and diversity. Relatively shallow water depths (≤13 cm) had greater abundance of shorebirds, wading birds, and geese, and higher diversity, whereas intermediate depths (~23 cm) resulted in the greatest dabbling duck abundance. Duck, goose, and wading bird abundances were greatest and species richness and family diversity were highest 8 days after the onset of flooding in rice fields (typically late October), followed by a decline in bird use until 65-87 days post flooding, after which bird use increased slightly. Bird abundance and species diversity were lowest in rice fields with the greatest hunting intensity (≥3 days week-1). We identified several habitat variables that could be managed and prioritized by landowner incentive programs to increase bird use of winter-flooded rice, including water depth, variation in emergent vegetation height, mudflat habitat availability, rice check shape, hunting intensity, and post-harvest treatment of residual rice straw.

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USGS2024

Individual-based ecological particle tracking model (ECO-PTM) for simulating juvenile chinook salmon migration and survival through the Sacramento – San Joaquin Delta

Recovery of endangered salmon species in the Central Valley of California amidst prolonged drought and climate change necessitates innovative water management actions that balance species recovery and California's water demands. We describe an individual-based ecological particle tracking model (ECO-PTM) that can be used to assess the efficacy of proposed actions. Based on a random walk theory, the model tracks individual particles’ travel time, routing and survival in a flow field simulated by the Delta Simulation Model 2 hydrodynamic module (DSM2 HYDRO). The random walk particles are parameterized to have fish-like swimming behaviors, including upstream/downstream swimming, probabilistic holding behaviors, and stochastic swimming velocities. Particle routing at key junctions is based on well-established statistical models, and route-specific survival is calculated using the XT mean free-path length model. Behavioral parameters were estimated by fitting several competing models to a multiyear dataset of travel times from acoustic tagged juvenile salmon. The model’s baseline simulations under historical flow conditions from 1991 to 2016 successfully replicated essential relationships between salmon outmigration survival and hydrodynamic conditions, consistent with previous studies and the STARS (Survival Travel Time and Routing Simulation) statistical simulation model. Simulation results for management scenarios revealed multifaceted influences on fish survival, including Delta flow, flow at key junctions, route alterations, seasons, and water year characteristics. Importantly, these results highlight ECO-PTM’s potential to predict fish survival outcomes of proposed actions, serving as a foundation for informed future research, decision-making, and effective management strategies to enhance the survival prospects of out-migrating salmonids within the Sacramento-San Joaquin Delta ecosystem.

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USGS2025

Combining ecological and genomic diversity surveys to inform conservation and restoration of an endangered wetland plant, soft salty bird’s-beak (Chloropyron molle ssp. molle)

Emergent tidal wetlands are declining globally as a result of sea level rise and land use change. This habitat loss can keenly affect rare plant species within wetlands, and may require restoration to meet species recovery goals related to retaining populations throughout species' ranges. Soft salty bird’s-beak ( Chloropyron molle ssp. molle ) is a federally- and state-endangered hemi-parasitic plant that occurs at the upper marsh transition zone in the San Francisco Bay–Delta, California, USA. We combined field surveys to document habitat associations and trends in abundance with genomic surveys to understand patterns of genetic structure in this rare endemic. We found that C . molle ssp. molle persisted at nine previously occupied marsh sites, although four sites (Hill Slough, MOTCO East, Fagan Marsh, and Joice Island) were smaller in population size than when surveyed in the 1990s. Additionally, twelve sites contained plots with suitable but unoccupied habitat that could be further assessed for restoration. Genomic analysis of over 40,000 single-nucleotide polymorphisms (SNPs) and 253 individuals grouped C . molle ssp. molle into six to seven regional genetic clusters with isolation by distance, and confirmed that C . molle ssp. molle is genetically distinct from adjacent populations of its closest relative ( C . molle ssp. hispidum ). The western-most C . molle ssp. molle sites of Point Pinole and Fagan Marsh were the most genetically and geographically isolated and had the lowest genome-wide diversity. Heterozygosity in sets of genes associated with tidal elevation, salinity, and annual and summer precipitation varied independently across populations. Overall, these genomic patterns indicate that selecting donor sites with similar environmental conditions and utilizing composite seeding approaches from multiple sites could allow for local adaptation to a range of possible environmental conditions. This comprehensive survey of habitat and genomic patterns can allow for the development of restoration actions and build climate-adaptation planning to help prevent the loss of a rare plant.

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USGS2025

Marsh sediment in translation: A review of sediment transport across a natural tidal salt marsh in northern San Francisco Bay

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. Research on sediment transport to marshes is published in technical journals, but these scientific findings must be translated and communicated to inform critical decisions related to managing sediment in estuaries. We convened a diverse group of collaborators—including natural-resource managers, regulators, scientists, and restoration planners and practitioners—to review and interpret the results of previously published field investigations on and around the salt marsh at China Camp State Park in Marin County, California. We discussed and translated key results of those studies using new graphics and more accessible language. Here, we present a general introduction to the topic of sediment delivery to salt marshes, background descriptions of the China Camp marsh and the physical processes that we characterized there, key scientific conclusions, and proposed management implications. Key conclusions include (1) bay shallows are an important but variable source of marsh sediment, (2) flood tides and waves move sediment across the bay–marsh edge, (3) tidal creeks may not always import sediment to the marsh platform, and (4) protective effects of marsh vegetation depend on species and season. China Camp marsh is one of the last remaining pre-colonial salt marshes in the San Francisco Estuary and is unique in being relatively unmodified by humans and in retaining an unimpeded transition into natural uplands. Additional studies in a variety of marshes with different attributes and sediment regimes will broaden understanding of how best to conserve, manage, and restore tidal marshes that provide numerous ecosystem services to for humans and wildlife.

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USGS2025

Effects of flow on pesticides in water and zooplankton in the northern Sacramento-San Joaquin Delta

Zooplankton are a key food source for juvenile fishes in estuaries worldwide, including California’s Sacramento–San Joaquin Delta (hereafter Delta); both zooplankton quality and quantity are critical to ecosystem health. Zooplankton may be affected by pesticides in water and the food web, and the Delta is known to contain complex pesticide mixtures. In this study, we evaluated pesticide concentrations in water and zooplankton in the northern Delta during (1) the summer–fall of 2017, 2018, and 2019, which included periods of augmented pulse flows from agriculture tailwater, and (2) across a full seasonal cycle from May 2019 to March 2020. We quantified changes in pesticide concentration in response to environmental factors. We found that zooplankton showed more frequent detections of hydrophobic pesticides compared to more frequent detections of hydrophilic compounds in water. Pesticide concentrations were influenced by flow, pesticide application, and season, but the effects of these environmental factors differed by habitat (Sacramento River or Yolo Bypass Toe Drain). Pesticides in water responded similarly to environmental factors in the Sacramento River and Yolo Bypass, whereas pesticides in zooplankton responded differently. In water, we found more detections and higher concentrations at higher flows in the Yolo Bypass and Sacramento River, but responses to pesticide application varied by habitat. Alternatively, pesticide concentrations in zooplankton increased in the Yolo Bypass with increasing flow (correlated with flow pulses) and changed seasonally; whereas, pesticide concentrations in zooplankton in the Sacramento River decreased at higher flows, and decreased with or did not respond to higher pesticide application in the watershed. Our study suggests that augmented flows—particularly those using agricultural tailwater—may have unintended negative ecological effects that could partially offset benefits to the food web and fishes in the northern Delta, underscoring the complex interplay among factors that drive increased pesticide exposure.

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USGS2025

Predicting sediment bulk density for San Francisco Estuary

Sediment bulk density (ρ-dry) and particle size are two important parameters for predicting sediment bed erosion. ρ-dry, however, is difficult to measure accurately. The units of ρdry have not been consistently reported in the literature, leading to confusion, particularly in the calculation of sediment budgets that typically require integrating mass-based and volumetric components. Relationships between ρdry and sediment composition have been developed for multiple regions and differ between systems. Developing a system-specific predictive model for ρdry can help fill data gaps and improve sediment budgets, model accuracy, and estimates of quantities of sediment needed for restoration. In this study, we investigate whether ρdry in San Francisco Estuary can be predicted from organic carbon content or percent of fines, which are more easily or frequently measured than ρdry. We compiled sediment properties from samples collected over the past decade throughout the intertidal and subtidal regions of San Francisco Bay and the Sacramento–San Joaquin Delta to examine this relationship. Sample composition ranged from 2.18 to 99.97% fines (particles < 0.0625 mm), ρ-dry ranged from 0.22 to 1.60 g cm-3, and organic carbon ranged from 0.06 to 7.98%. Regression analysis indicates that the percent of fines explains 93% of the variation of ρ-dry ( p -value < 0.05, N = 81). The coefficient of determination decreased by ~1% when organic carbon was incorporated in the regression analysis. Comparison of this predictive ρ-dry model to four published models based on samples from other regions supports previous findings that the relationship between ρdry and grain size may vary by system. We also examined additional factors that may affect sediment erodibility, such as hydrographic and oceanographic conditions. Classification of sample sites as intertidal vs. subtidal or wavy vs. non-wavy each significantly explained the residuals from the ρdry model, and both intertidal and wavy conditions were associated with higher ρ-dry values.

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USGS2026

Assessment of Chinook Salmon smolt survival at offsite release locations in the Sacramento River across wet and dry years

We used acoustic telemetry to estimate survival of tagged release groups, and quantify differences between alternative hatchery release strategies. To assess whether offsite release could increase survival of hatchery fish relative to those released at the hatchery, we compare survival during emigration of hatchery fall Chinook Salmon (FCS, Oncorhynchus tshawytscha ) smolts released onsite, at Coleman National Fish Hatchery (NFH), to those released at alternative offsite locations downstream in the upper Sacramento River, California. Approximately 300 fish in each release group were implanted with acoustic tags in the 3-year study during 2019, 2021, and 2022. Environmental conditions in the emigration corridor varied between study years, with extended high flows in 2019, whereas drought conditions and a flat hydrograph occurred in 2021 and 2022. Survival across years appeared to reflect environmental conditions, with higher overall survival seen in 2019. Survival differences between release sites generally showed higher cumulative survival to Knights Landing or Chipps Island for the downstream release groups, compared to the onsite releases during 2021 and 2022. This information suggests hatchery releases of FCS from Coleman NFH at downstream release sites may benefit emigration survival during years of drought and sub-optimal in-river conditions, compared to standard onsite releases. Hatchery managers can use information from this study to diversify the portfolio of release strategies, which may be useful to buffer against extreme variations of adult abundance by spreading risks across space and time. Ultimately, offsite releases may be a useful tool for adaptive management of these culturally, ecologically, and economically important salmon populations.

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