Recent jmie_sfews items

Flooded Wetland Availability for Breeding Waterfowl in a Mediterranean Climate: Mapping 38 Years of Historical Data in Suisun Marsh, California

Wed, 26 Nov 2025 00:00:00 +0000

Most managed wetlands in California are ephemeral and are purposefully flooded during the fall and winter for over-wintering waterfowl and are dry during the spring and summer waterfowl breeding season. Only semi-permanent and permanent wetlands remain flooded through the critical summer brood-rearing period for ducklings. We examined flooded wetland availability for breeding waterfowl in the brackish Suisun Marsh (California, USA) annually during the spring (April 27–May 17, during peak nesting) and summer (June 17–July 7, during peak duckling brood rearing), for a 38-year period using Landsat satellite imagery and spectral mixture analysis. Flooded wetland area increased 43% in spring and 48% in summer from 1984 to 2021 but varied among years (spring: 37.6–88.6 km²; summer: 17.7–57.5 km²). This increase in flooded wetland area over the past four decades was due to just a few sites, with only 24% (spring) and 15% (summer) of the 198 land-owner parcels...

Restoring the Heart of a Healthy Estuary: A Review of Restoration in the Sacramento–San Joaquin Delta and Suisun Marsh

Wed, 26 Nov 2025 00:00:00 +0000

The restoration of native species-dominated ecosystems is critical for improving ecosystem health and meeting policy goals in the Sacramento–San Joaquin Delta and Suisun Marsh (upper San Francisco Estuary, collectively), one of the largest estuarine systems in North America. To accomplish large-scale restoration in this heavily altered system, a variety of projects, programs, and motivations inform restoration planning and implementation. Chapter 4 of the Delta Plan synthesizes restoration goals across these efforts to produce comprehensive ecosystem restoration targets of between 60,000 and 80,000 acres across seven ecosystem types by 2050, but a comprehensive review of restoration progress and planning to date is needed. To fill this gap, this paper analyzes the current state of ecosystem restoration in the upper San Francisco Estuary in the context of the Delta Plan targets. We review current scientific and management literature and implementation approaches, and synthesize...

Predicting Sediment Bulk Density for San Francisco Estuary

Tue, 25 Nov 2025 00:00:00 +0000

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...

Synthesizing Relationships Between Winter-Run Chinook Salmon Out-Migration Survival and Water Operations in the Sacramento–San Joaquin Delta

Tue, 25 Nov 2025 00:00:00 +0000

Sacramento River winter-run Chinook Salmon (Oncorhynchus tshawytscha) are an endangered population that faces numerous challenges across its life cycle, including juvenile out-migration through the heavily anthropogenically modified Sacramento–San Joaquin Delta, or Delta. Water exports from pumping facilities in the Delta can alter local hydrology and influence movement of out-migrating juveniles, some of which are observed in or near pumping facilities. Monitoring and regulations, intended to protect out-migrating fish through restrictions on pumping, are predicated on assumed relationships among fish observations, water operations, and through-Delta migratory survival. In this study, we use a new conceptual model to review the current state of science for winter-run Chinook Salmon out-migration survival in the Delta, and use simulation modeling to address pertinent knowledge gaps. Results of this study highlight varying support for the influence of Sacramento River...

The Influence of Zooplankton Availability on Delta Smelt Condition and Foraging Across Habitat Contexts

Tue, 25 Nov 2025 00:00:00 +0000

Strategies for endangered species conservation may have different outcomes depending on the habitat context in which they are implemented. Understanding these context-dependent effects can help optimize and target management efforts. In this analysis, we investigate how environmental and food-web conditions interactively affect condition and foraging of Delta Smelt (Hypomesus transpacificus), an endangered fish endemic to the San Francisco Estuary (the estuary). Food limitation, in terms of pelagic zooplankton availability, is considered a main factor that contributes to the decline in Delta Smelt abundance. Our overarching objective was to examine whether the effect of zooplankton on Delta Smelt depended on habitat context. Specifically, we hypothesized that zooplankton would less positively effect Delta Smelt condition—as measured by hepatosomatic index (HSI)—and foraging success in areas with nearby tidal wetlands, because these adjacent habitats may provide access...

Effects of Flow on Pesticides in Water and Zooplankton in the Northern Sacramento–San Joaquin Delta

Tue, 25 Nov 2025 00:00:00 +0000

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...

Estimating Freshwater Inflow to San Francisco Estuary During the First Six Decades Following the California Gold Rush: WYs 1851–1911 Reconstruction Based on Legacy Hydrologic Data

Sun, 24 Aug 2025 00:00:00 +0000

Freshwater inflow is vital for the ecological health of estuaries. Understanding historical flow volume and timing is therefore essential for sustainable management and restoration of these environments. Using legacy hydrologic data—including riverine water-level measurements, watershed runoff estimates, and wetland reclamation records—we extended a monthly time-series of freshwater inflow to San Francisco Estuary by 6 decades, back to California’s Gold Rush era. This period marks the onset of significant anthropogenic modifications to the waterscape. Our analysis of the extended series, normalized to unimpaired runoff, reveals an increasing trend in systemwide water use that was preceded by a decline in the latter half of the 19th century. We hypothesize this decline resulted from reduced evapotranspiration as a result of vegetation removal and reduced overbank flows from levee construction. These findings align with earlier research that shows similarities between natural and...

Integrating Hydrodynamics and Fish Vital Rates into Indices of Entrainment for Endangered Smelts at the Barker Slough Pumping Plant

Sat, 23 Aug 2025 00:00:00 +0000

Fish losses to entrainment in water diversions in the Sacramento–San Joaquin Delta have been a long-standing conservation concern. We evaluated Delta Smelt (Hypomesus transpacificus) and Longfin Smelt (Spirinchus thaleichthys) entrainment risk associated with the Barker Slough Pumping Plant (BSPP) by integrating hydrodynamic, growth, survival, and fish-screen-selectivity information into indices of entrainment risk for nine locations in the Cache Slough Complex (CSC). Our fundamental question was: How does risk of entrainment into BSPP vary in space and time? We found the predicted risk of entrainment into BSPP is extremely high from the adjacent Lindsey Slough. From elsewhere in the CSC, entrainment risk into BSPP is approximately zero in both wet and dry years, such that local irrigation diversions are the only potential source of entrainment loss. We estimated Delta Smelt outgrow vulnerability to entrainment through the BSPP fish-screens in 35 to 53 days while Longfin Smelt...

Atmospheric Rivers and Floods in California’s Changing Hydroclimate

Sat, 23 Aug 2025 00:00:00 +0000

Flooding in the Bay–Delta is most commonly due to runoff from atmospheric river (AR) storms, often enhanced by low-elevation snowmelt. In this paper, we review the current science of ARs and their projected enhancement in a warming climate. We also address the changing state of the Sierra Nevada snowpack. Climate-model projections indicate increasing contributions to extreme precipitation from ARs, and more variable hydroclimate, with increased floods as well as droughts. Observations, meanwhile, do not yet show enhanced precipitation intensity trends. In agreement with climate-model projections, observations do show that, as the climate continues to warm, California’s greatest natural freshwater reservoir—its snowpack—continues to erode. This is despite record snowpacks (e.g., 2023) still being possible, and potentially exacerbating flood effects from ARs in a highly variable hydroclimate. Original analysis of extreme historical and projected precipitation events shows events...

Recent Findings and Future Prospects for Water Quality Effects from Catastrophic Wildfires in California, USA

Sat, 23 Aug 2025 00:00:00 +0000

Global change affects the forests and wildlands of California through rising temperatures, earlier snowmelt, more rain and less snow, greater vapor-pressure deficits, and forest dieback, resulting in increased frequency, size, and severity of wildfires. California has experienced its eight largest wildfires since 1932 in the period from 2018 to 2024. The largest fire to date (August Complex Fire) occurred in 2020—a year in which 1.7 million ha or 4% of California’s land area burned—and burned 418,000 ha. These mega-fires (>10,000 ha) can severely affect water quality and aquatic ecosystems. Water-quality variables affected by wildfire include temperature, sediment load, turbidity, dissolved oxygen, pH, redox potential, soluble and particulate organic carbon, nutrients, metals, natural- and human-produced organic contaminants, and primary/secondary producers. Wildfire and water interact at watershed scales, with water-quality impairments responding linearly with the percentage...

Five Perspectives to Advance Science-Informed Decision-Making in the Era of Climate Change and Extreme Events

Fri, 22 Aug 2025 00:00:00 +0000

California’s variable hydroclimate is projected to become increasingly volatile in the 21st century. Yet, there is widespread recognition that extreme events, such as record-breaking heatwaves and catastrophic wildfires, are already becoming the new normal. The 2025 edition of the State of Bay–Delta Science (SBDS) presents the current state of the science on climate change and extreme events affecting the Delta and its watershed, and in doing so, generates new insights on knowledge gaps and promising directions for future research. In this essay we present five perspectives to advance science-informed decision-making in the era of climate change and extreme events. To meet these challenges, Delta scientists and decision-makers can leverage the many effective practices that are already in place, such as long-term monitoring programs, collaborative synthesis venues, science-informed decision-making processes, and Tribal and community partnerships. New and sophisticated tools that...

Changing Paradigms of Knowledge Production: Interweaving Traditional Knowledge and Predominant Science in the Delta

Sat, 22 Mar 2025 00:00:00 +0000

Abstracts are not associated with Essays. —the SFEWS Editors

Combining Ecological and Genomic Diversity Surveys to Inform Conservation and Restoration of an Endangered Wetland Plant, Soft Salty Bird’s-Beak

Sat, 22 Mar 2025 00:00:00 +0000

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...

Thermal Stress and Suitability for Aquatic Species in the San Francisco Estuary

Sat, 22 Mar 2025 00:00:00 +0000

Increases in water temperature caused by climate change will challenge the management of water and species in the San Francisco Estuary. Our goals were to describe spatial and seasonal patterns in water temperature across the upper estuary, and evaluate how temperature stress and suitability vary across the aquatic ecosystem. We synthesized 10 years of continuous water-temperature data at 75 stations across six regions of the estuary between 2010 and 2019. We identified stressful temperature thresholds for species of interest using published physiological limits and observed distributions, including Endangered Species Act-listed native fishes (e.g., osmerids, salmonids), native fishes (e.g., cyprinids), non-native species (e.g., centrarchids, bivalves), and nuisance species such as invasive aquatic vegetation, and harmful cyanobacteria. We then quantified thermal stress across varying spatial and temporal scales and metrics. Analyses indicated there were detectable regional temperature...

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

Sat, 22 Mar 2025 00:00:00 +0000

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...

Genetic Assessment of Floodplain Habitat Use by Juvenile Chinook Salmon

Sat, 22 Mar 2025 00:00:00 +0000

Climate change is having widespread negative effects on freshwater environments, including an increasing frequency and severity of droughts. Drought conditions present unique challenges for the federally listed Central Valley Chinook Salmon (Oncorhynchus tshawytscha), which use the already limited floodplain in the Central Valley as rearing habitat. In this study, we examined how differing hydrologic conditions influence the run composition of juvenile Chinook Salmon in the floodplain (Yolo Bypass) versus the mainstem of the Sacramento River. Juvenile Chinook Salmon from the Yolo Bypass and areas along the Sacramento River were identified to the genetically distinct runs (fall, late fall, winter, and spring) from 2013-2019. We found overwhelmingly that Length at Date methods are misclassifying fish, particularly late fall and spring run fish, and winter-run fish in the bypass. Using this genetic run-timing, we found that the abundances of endangered runs (spring and winter) are...

Multiple-Benefit Conservation in Practice: A Framework for Quantifying Multidimensional Effects of Landscape Change in California’s Sacramento–San Joaquin Delta

Sat, 22 Mar 2025 00:00:00 +0000

Conservation efforts and other land-management decisions are often intended to provide multiple benefits, but real or perceived trade-offs between goals can increase conflict and limit the practice of Multiple-Benefit Conservation. To support decision-making, policy, and management in the Sacramento–San Joaquin River Delta of California, where multiple potentially conflicting goals and values have been identified, we developed a flexible framework for quantifying the benefits and trade-offs that result from landscape change, implemented as an open-source R package. Integrating multiple data sets and methods, we developed metrics that represent (1) agricultural livelihoods, (2) water quality, (3) climate-change resilience, and (4) biodiversity support benefits and then projected the net effects on each metric of three alternative Delta landscapes. Each alternative represented changes that could result by 2050 from meeting habitat-restoration targets in the Delta Plan for riparian...

Drought in the Delta: Socio-Ecological Impacts, Responses, and Tools

Tue, 18 Mar 2025 00:00:00 +0000

Droughts are frequent events in the western United States, and can disrupt water supply and degrade water quality, challenging water management in the Sacramento–San Joaquin Delta (Delta). This chapter for the State of Bay–Delta Science report describes what drought means for the Delta, how drought is managed in the Delta, and how drought management has changed over time. Projections of future climate indicate the possibility of increased frequency and severity of droughts which would have increasing effects on California’s water system, society, and ecological functions within and beyond the Delta. California has experienced several major droughts in the 20th and 21st centuries, each of which has caused significant social and ecological impacts and motivated improvements in water management. Droughts decrease native fish populations, increase harmful algal blooms, and promote the spread of many invasive plant and animal species. For people living within the Delta and those that...

Assessing Fish Distribution in Richardson Bay, California: A Preliminary Dual-Frequency Identification Sonar and Environmental Data Approach

Mon, 17 Mar 2025 00:00:00 +0000

Estuaries provide critical habitat for many economically and ecologically valuable species that are adapted to a wide range of conditions and environmental variability, but the often turbid water presents challenges to monitoring efforts. This study explored fish habitat use in Richardson Bay, California (a sub-estuary of San Francisco Bay) at two points in time: one following a dry winter (2016) and the other following a historically wet winter (2017). Dual-frequency Identification Sonar (DIDSON) was used to record finfish and ray (>10 cm) abundance (MaxN) and size distribution, putative ray foraging pit size and abundance (MaxN), and eelgrass (Zostera marina) presence. We measured temperature, salinity, and dissolved oxygen (DO) at each site, and water samples at a subset of sites for nutrient analysis (urea, ammonium, nitrate, silicate, phosphate). Relationships between these data were explored using an information-theoretic modeling approach. Finfish abundance was best...

Heatwaves and Rising Temperatures in the Upper San Francisco Estuary: Trends and Effects on Ecosystems and Humans

Mon, 17 Mar 2025 00:00:00 +0000

Rising temperature is one direct consequence of climate change, and temperature is a key controlling variable on biological processes from molecular to ecosystem scales. While rising average temperature is one of the most discussed aspects of climate change, extreme events such as heatwaves are also expected to increase in duration, intensity, and frequency. These changes will bring about effects that threaten the integrity of the upper San Francisco Estuary (estuary) ecosystem, the services they provide to humans, and the health of humans that reside in the region. In the estuary, warmer temperatures are expected to result in seasonal shifts to life-cycle timing, and to favor smaller-bodied individuals across most non-human taxa. Several native fish species will likely decline, while a considerable number of non-native and cosmopolitan species tolerant of high temperatures are predicted to be relatively unaffected by or even benefit from a warmer climate. For humans, high temperatures...

Assessing the State and Efficacy of Climate Governance Research and Practice in the Sacramento–San Joaquin Delta

Mon, 17 Mar 2025 00:00:00 +0000

Climate change affects nearly every aspect of the interdependent biophysical and social systems in California’s Sacramento–San Joaquin Delta. Mitigating and adapting to these effects will require effective climate governance: referring to the actors, rules, and processes through which decisions are made to prevent and respond to climate change. How governance systems effectively achieve these goals has become an increasingly central question in climate social science and climate policy debates, both at global and local scales. This paper reviews the state of science on climate governance in the Delta and investigates the extent to which effective climate governance characteristics operate in this region. The literature on climate governance broadly distills two key dimensions that scholars suggest influence efficacy: the structure of a governance system (e.g., extent of centralization and decentralization and mechanisms for coordination) and the degree of reactivity or proactivity...

The State of Bay–Delta Science: An Introduction to the 2025 Extreme Events Edition

Mon, 17 Mar 2025 00:00:00 +0000

The State of Bay–Delta Science (SBDS) is intended to inform science and policy audiences about the “state of the science” for topics relevant to management of the San Francisco Bay and Sacramento–San Joaquin Delta (“Bay–Delta”) system. When referencing the Bay–Delta system, we include the atmosphere, watershed, politics, and governance at a broad scale. Each SBDS edition has communicated new insights on a range of high-priority issues by synthesizing the current science and discussing progress on key research questions, knowledge gaps, and proposed future research. Collectively, these editions provide valuable summaries of the physical, biological, and social dimensions of the Bay–Delta. The first edition in 2008 provided a system-wide baseline on history, geography, water quality, ecosystem restoration, levee integrity, water supply, and public policy issues in the Bay–Delta (Healey et al. 2008). Eight years later, the second edition featured research on a dozen priority topics...

Individual-Based Ecological Particle Tracking Model (ECO-PTM) for Simulating Juvenile Chinook Salmon Migration and Survival Through the Sacramento–San Joaquin Delta

Mon, 9 Dec 2024 00:00:00 +0000

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...

Investigation of Floating Peat Wetlands, Sacramento–San Joaquin Delta, California

Mon, 9 Dec 2024 00:00:00 +0000

Tidal wetland restoration is integral to achieving the Delta coequal goals. Deeply subsided islands limit the potential for tidal wetland restoration. Floating peats may offer an opportunity to create tidal habitat in the subsided western and central Delta. We conducted a mesocosm experiment to assess the feasibility of floating peat blocks, and the potential food-web benefits, biomass production, carbon sequestration, methane emissions, and water-quality effects. We evaluated the effect of varying water residence time and initial peat-block density.

The peat blocks floated during the entire experiment, and accreted biomass at rates consistent with those reported for Delta non-tidal managed wetlands. Peat blocks placed in mesocosms with 45% open water expanded horizontally about 21% per year. We estimated average vertical accretion rates of 5.5 to 8.6 cm/yr for all the mesocosms. Vertical and horizontal expansion increase floating peat-block stability.

We...

Management of Tidal Wetland Restoration and Fish in the Upper San Francisco Estuary: Where are We Now and How Do We Move Forward? A Summary of the 2023 Wetland Science Symposium

Mon, 9 Dec 2024 00:00:00 +0000

Tidal wetland restoration to benefit at-risk fish species in the Sacramento-San Joaquin Delta and Suisun marsh has gained momentum over the past decade, much of it in response to mitigation requirements for the State Water Project and Central Valley Project. In fall 2023, the Department of Water Resources and the State Water Contractors convened a symposium, entitled Delta-Suisun Tidal Wetland Restoration Symposium: State of the Science and Future Directions, to discuss the latest wetland restoration research and future directions. The symposium was held 10 years after the 2013 symposium “Tidal Marshes and Native Fishes in the Delta: Will Restoration Make a Difference?”, so served as an opportunity to follow up on the progress that has been made over the past decade. This paper synthesizes the key findings from the 2023 workshop.

The paper begins with the historical context of wetland restoration in the Delta and Suisun marsh, then outlines the restoration process as...

Nine Takeaways from a Quarter Century Working with the Interagency Ecological Program

Mon, 9 Dec 2024 00:00:00 +0000

< Abstracts are not associated with Essays. -the SFEWS Editors. >

Every Cog and Wheel: Identifying Biocomplexity at the Genomic and Phenotypic Level in a Population Complex of Chinook Salmon

Mon, 9 Dec 2024 00:00:00 +0000

Genetic diversity is the fundamental building block of biodiversity and the necessary ingredient for adaptation. Specifically, the intra-specific diversity (biocomplexity) comprised of phenotypic and genetic variation partitioned within and among populations can determine the ability of a species to respond to changing environmental conditions. Here, we explore the biocomplexity of California’s Central Valley Chinook salmon (Oncorhynchus tshawytscha) population complex at the genomic level by quantifying population genomic diversity among and within migration life-history phenotypes. Notably, despite apparent gene flow among populations with the same migration (life history) phenotypes inhabiting different tributaries, each group is characterized by a distinct component of unique genomic diversity. While enumerating biodiversity contained within individual hierarchical levels is informative, it is important to consider inter- and intra-specific diversity simultaneously...

Seasonal and Size-Specific Occupancy of Striped Bass in the Stanislaus River, California

Mon, 5 Aug 2024 00:00:00 +0000

Striped Bass (Morone saxatilis) monitoring and research in California’s Central Valley primarily occurs in the Sacramento River basin and the Sacramento–San Joaquin Delta. A relatively under-studied contingent of the Striped Bass population is present in the San Joaquin River and its tributaries. One such tributary, the Stanislaus River, is an important source of natural production of native anadromous fishes, including fall-run Chinook Salmon (Oncorhynchus tshawytscha), Steelhead (O. mykiss), and Pacific Lamprey (Entosphenus tridentatus). Because Striped Bass are a non-native piscivore, characterizing when and where their distribution overlaps with native fishes is a first step to assessing the potential for negative inter-specific interactions. We compiled incidental observations of Striped Bass made during long-term (1996 to 2021) salmonid monitoring programs performed at different times of the year, and found that Striped Bass were present...

Status and Trends of Breeding Ardeidae in the San Francisco Bay Region

Mon, 5 Aug 2024 00:00:00 +0000

Abstract: Monitoring species abundance is a critical tool for identifying trends in wildlife populations. Using data collected in the San Francisco Bay Area between 1995 and 2019, we evaluated trends in nesting abundance of four Ardeid species across the entire study area and in 10 subregions, while accounting for the effect of rainfall. Overall, Great Egret (Ardea alba) nest abundance increased by 27% (95% confidence interval -1%, 54%) from 783 to 993 nests. Great Blue Heron (Ardea herodias) and Snowy Egret (Egretta thula) nesting abundance was similar across the study period, averaging approximately 503 and 509 nests, respectively, but Snowy Egret abundance was highly variable between years. Finally, Black-crowned Night-Heron (Nycticorax nycticorax) abundance declined -22% (95% confidence interval -59%, 15%) from 682 to 535 nests. At the subregional scale, trends were variable within species, and no species had consistent positive or negative...

Surveying Waterfowl Broods in Wetlands Using Aerial Drones

Mon, 5 Aug 2024 00:00:00 +0000

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 that encompassed 332ha of flooded area on the premises of seven waterfowl hunting clubs during the waterfowl breeding season. Additionally, using a combination of multi-spectral 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 comprising 827 ducklings. We found a positive relationship...

Bird Habitat Value and Management Priorities of the California Winter Rice Habitat Incentive Program

Mon, 5 Aug 2024 00:00:00 +0000

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 that influence 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...

Climate Change Scenarios for Air and Water Temperatures in the Upper San Francisco Estuary: Implications for Thermal Regimes and Delta Smelt

Tue, 4 Jun 2024 00:00:00 +0000

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...

Managed Wetlands for Climate Action: Potential Greenhouse Gas and Subsidence Mitigation in the Sacramento–San Joaquin Delta

Tue, 4 Jun 2024 00:00:00 +0000

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...

Sub-Lethal Responses of Delta Smelt to Contaminants Under Different Flow Conditions

Tue, 4 Jun 2024 00:00:00 +0000

The Delta Smelt is a largely zooplanktivorous, endangered fish endemic to the San Francisco Estuary (the estuary). High flows increase the availability of fresh and brackish water habitat for Delta Smelt, but also may mobilize contaminants, potentially increasing toxicological stress. Here, we examine the association between contaminants and Delta Smelt health across contrasting water year types and flow-related management actions. Our study spanned the fall season of three years: 1 dry year (2018) bracketed by 2 wet years (2017 and 2019) and coincided with several management actions meant to benefit Delta Smelt. We collected field water from six sites in the estuary that encompass the freshwater and low-salinity habitat of Delta Smelt and analyzed the water for contaminant concentrations. After a 96-hour exposure to the field water, we assessed cultured Delta Smelt survival and the histopathological condition of the gill and liver. Insecticides, particularly fipronil metabolites,...

Spatial Patterns of Water Supply and Use in California

Tue, 4 Jun 2024 00:00:00 +0000

Spatial and temporal patterns of water supply and consumptive water use were analyzed from 475 Detailed Analysis Units by County (DAUCOs) spatial units across California during 2002 through 2016 to evaluate spatial and temporal variability and how it might associate with precipitation variability and other factors. Many, but not all, DAUCOs have relatively low total water supply variability compared to that of state-wide precipitation. Such low variability, in DAUCOs having sufficient diversity of water supply sources, is the result of switching between sources as needed to maintain a reliable total water supply. We used multiple approaches to explore these variations which involved four categories of water supply (local, groundwater, imported, and other) and two categories of water use (agricultural and urban). First, a cluster analysis of the volumetric water balance data identified a small set of clusters having similar magnitudes and proportions of water supply sources and...

Regional Diversity Trends of Nearshore Fish Assemblages of the Upper San Francisco Estuary

Tue, 4 Jun 2024 00:00:00 +0000

The loss of biodiversity and biotic homogenization are on the rise in ecosystems around the world as a result of species invasions, habitat degradation, and the effects of climate change. In the Sacramento–San Joaquin Delta, non-native species make up the majority of the fish community, and declines in native species have been well documented; however, little is known about whether these trends have resulted in biotic homogenization. In this study, we used data from a long-term beach seine survey to analyze regional beta diversity trends of nearshore fish assemblages in the Delta from 1995 to 2019. Overall, we found no evidence of regional biotic homogenization occurring over the study period. Regional beta diversity increased moderately over time and was significantly influenced by the high interannual variability of freshwater inflow. These beta diversity patterns were driven by the non-native Mississippi Silverside that has proliferated in the system in recent years, but also...

Years of Drought and Salt: Decreasing Flows Determine the Distribution of Zooplankton Resources in the San Francisco Estuary

Mon, 18 Mar 2024 00:00:00 +0000

The San Francisco Estuary (estuary) and the Sacramento–San Joaquin Delta (the Delta) in California face significant challenges in managing water resources during extended droughts. Zooplankton are a vital trophic link between phytoplankton producers and higher-level consumers such as predatory zooplankton and fish. However, there is still much to be learned about what drives zooplankton abundance and how they respond to drastic changes in environmental conditions, such as droughts. We found that during drought years zooplankton abundance and distribution changes varied for examined taxa. Significant declines in the abundance of Daphnia spp. and the copepod Pseudodiaptomus forbesi occurred in the Suisun Marsh and Suisun Bay regions. In contrast, abundance of the non-native copepod Limnoithona tetraspina increased in Suisun Marsh and the South-Central Delta during those same drought conditions. Salinity is a strong determinant of the presence and abundance...

Amazing Graze: Shifts in Jellyfish and Clam Distributions During Dry Years in the San Francisco Estuary

Mon, 18 Mar 2024 00:00:00 +0000

Aquatic invasive species have drastically changed how the San Francisco Estuary functions. During the past 2 decades, the effects of invasive species in the estuary may have increased in response to frequent and severe drought conditions. The invasive overbite clam (Potamocorbula amurensis), and the Asian clam (Corbicula fluminea) have well documented consequences on the estuarine food web, but their responses to drought are not well understood. Another invasive species, the jellyfish Maeotias marginata, can further affect the food web, but these effects have not been studied. We investigated the population responses of these invasive species to dry years and their potential effects on the pelagic food web using data from the Interagency Ecological Program’s monitoring surveys. We found M. marginata rapidly moves upstream with changing salinities during dry years, though it sees its highest abundance during high-outflow years in...

Delta Blue(green)s: The Effect of Drought and Drought-Management Actions on Microcystis in the Sacramento–San Joaquin Delta

Mon, 18 Mar 2024 00:00:00 +0000

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...

Dry Me a River: Ecological Effects of Drought in the Upper San Francisco Estuary

Mon, 18 Mar 2024 00:00:00 +0000

Droughts have major effects on estuaries because freshwater entry is one of the defining features of an estuary, and freshwater flow is an important variable that determines the interannual change in the environment. In the upper San Francisco Estuary (the Sacramento–San Joaquin Delta, Suisun Bay, and Suisun Marsh), the Mediterranean climate includes frequent multi-year droughts. To assess ecosystem responses to droughts in the upper estuary, the Interagency Ecological Program Drought Synthesis Team assembled a set of flow, water quality, chlorophyll, zooplankton, and fish data from 1975 to 2021 to test for differences between multi-year droughts and multi-year wet periods and tested for linear relationships between each variable and the Sacramento Valley Hydrologic Index (see definitions and relationships as outlined in Appendix A). Our models showed droughts decreased Delta outflow, project exports, zooplankton in Suisun Bay, and some fish species. We also found that droughts...

The Anatomy of a Drought in the Upper San Francisco Estuary: Water Quality and Lower-Trophic Responses to Multi-Year Droughts Over a Long-Term Record (1975-2021)

Mon, 18 Mar 2024 00:00:00 +0000

Multi-year droughts are ever-present and transformational features of California’s Mediterranean climate and can fundamentally affect the water quality and the ecosystem responses of the San Francisco Estuary and the Sacramento–San Joaquin Delta. This study assessed data collected by long-term monitoring programs over the past 46 water years (1975–2021) to evaluate how water quality in the estuary changes during multi-year droughts. Data were aggregated by region (South-Central Delta, North Delta, confluence, Suisun Bay, and Suisun Marsh) and season, then differences between multi-year drought periods, multi-year wet periods, and neutral periods were compared using generalized linear models. We found that multi-year drought periods altered 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...

Comparing Fishery Impacts and Maturation Schedules of Hatchery-Origin vs. Natural-Origin Fish from a Threatened Chinook Salmon Stock

Fri, 15 Dec 2023 00:00:00 +0000

Central Valley Spring-run Chinook (CVSC) are listed as threatened under the California and federal Endangered Species Acts, but how ocean fisheries affect CVSC is not routinely monitored or managed , largely because of data limitations. Most tag data for CVSC are from a hatchery program that may not sufficiently represent natural-origin fish in ocean and inland fishery recovery data. However, a discontinued tagging program for Butte Creek Wild Spring-run Chinook (BCWSC) provides for estimation of fishery impacts and maturation schedules for a limited set of years, which we compared with estimates for hatchery-origin fish for common years, while extending the hatchery-origin estimates over a wider time-frame. Additional scale-age data from BCWSC allow inferences about more recent maturation rates, conditional on harvest-rate estimates borrowed from other stocks. Overall, CVSC appear to experience low age-3 ocean fishery impact rates, but age-4 impact rates can be comparable to...

Keeping Water in Climate-Changed Headwaters Longer

Fri, 15 Dec 2023 00:00:00 +0000

Abstracts are not associated with Essays. –the SFEWS Editors

A Simple Approach to Modeling Light Attenuation in the Sacramento–San Joaquin Delta Using Commonly Available Data

Fri, 15 Dec 2023 00:00:00 +0000

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...

A Simplified Approach for Estimating Ionic Concentrations from Specific Conductance Data in the San Francisco Estuary

Fri, 15 Dec 2023 00:00:00 +0000

This work presents a simplified approach for estimating ionic concentrations from specific electrical conductance (EC) data in the San Francisco Estuary. Monitoring the EC of water through electrodes is simple and inexpensive. As a result, a wealth of high-resolution time-series data is available to indirectly estimate salinity concentrations and, by extension, seawater intrusion throughout the study domain. However, scientists and managers are also interested in quantifying ionic (e.g., bromide, chloride) and total dissolved solids (TDS) concentrations to meet water-quality regulations, protect beneficial uses, support environmental analyses, and track source-water dominance. These constituent concentrations, reported with lower spatial and temporal resolution than EC, are typically measured in the laboratory from discrete (grab) water samples. We divided the study domain into four unique regions to estimate concentrations of major ions and TDS as mathematical functions of measured...

Proofing Field and Laboratory Species Identification Procedures Developed for the Non-Native Osmerid Species Wakasagi (Hypomesus nipponensis) Using SHERLOCK-Based Genetic Verification

Fri, 15 Dec 2023 00:00:00 +0000

Accurate species identification is critical to monitoring programs because mis-identifications can lead to incorrect assessments of population status and trends. In the San Francisco Estuary, efforts to monitor the imperiled osmerid Delta Smelt (Hypomesus transpacificus) using morphology can be challenging because of the presence of the similar-looking non-native osmerid Wakasagi (Hypomesus nipponensis). In 2017, the US Fish and Wildlife Service’s field office in Lodi implemented a two-stage verification process for Wakasagi to help prevent Delta Smelt from being mis-identified as Wakasagi. Under this process, Wakasagi are initially identified in the field, independently identified a second time by an experienced staff member in the laboratory, then stored on-site where they can be made available for future studies. Using the recently developed Specific High-sensitivity Enzymatic Reporter un-LOCKing (SHERLOCK) assay for Wakasagi, we evaluated how well verification...

Diets of Native and Non-Native Piscivores in the Stanislaus River, California, Under Contrasting Hydrologic Conditions

Fri, 15 Dec 2023 00:00:00 +0000

The fish communities of the Sacramento–San Joaquin Delta and its tributaries in California’s Central Valley have been irreparably altered through introductions of numerous fish species, including Striped Bass (Morone saxatilis), black bass (Micropterus spp.), and catfishes (Ameiurus spp. and Ictalurus spp.). Research into how predation by non-native piscivores affects native anadromous species has focused on the Sacramento and San Joaquin river mainstems and Delta habitats, through which all anadromous species must pass. Yet, the ranges of non-native fishes extend into upstream tributaries. We collected diets from native and non-native piscivores in the Stanislaus River, a tributary to the San Joaquin River and a remaining stronghold for native fishes. Piscivorous fishes primarily consumed invertebrates and the native species fall-run Chinook Salmon (Oncorhynchus tshawytscha) and Pacific Lamprey (Entosphenus tridentatus). Juvenile...

Priority Bird Conservation Areas in California’s Sacramento–San Joaquin Delta

Mon, 28 Aug 2023 00:00:00 +0000

Conserving bird populations is a key goal for management of the Sacramento–San Joaquin Delta ecosystem and is likely to have effects well beyond its boundaries. To inform bird- conservation strategies, we identified Priority Bird Conservation Areas for riparian landbirds and waterbirds in the Delta, defined as the most valuable 5% of the landscape for each group. We synthesized data from 2,547 surveys for riparian landbirds and 7,820 surveys for waterbirds to develop predictive distribution models, which then informed spatial prioritization analyses. We identified a total of 26,019 ha that are a high priority for conserving riparian landbirds, waterbirds, or both, representing the most important places in the Delta to protect and manage, as well as strategic areas where adjacent restoration could expand valuable habitat. These Priority Bird Conservation Areas include the Yolo Bypass Wildlife Area, Cosumnes River Preserve, Stone Lakes National Wildlife Refuge, and bufferlands that...

A Qualitative Comparison of Spawning Behavior between Cultured and Wild Delta Smelt (Hypomesus transpacificus)

Mon, 28 Aug 2023 00:00:00 +0000

For many imperiled species, comparisons between wild and cultured populations are invaluable for informing conservation measures, though opportunities to do so may be rare. In this study, we asked whether spawning between and among wild and cultured Delta Smelt varies in terms of behavior or resulting egg fertilization success. We conducted two laboratory experiments in which we allowed wild females to spawn with wild males (wild × wild) and cultured females to spawn with wild males (cultured × wild). Due to small sample sizes, we qualitatively compared our results to published studies of all cultured Delta Smelt (cultured × cultured). Across all three groups, Delta Smelt exhibited spawns that were similar in sequence and manner, varied widely in diel timing, and occurred predominantly between a single female and one or two males. Egg fertilization success was higher in wild × wild trials than in cultured × wild ones, but both...

Long-Term Trends in Seasonality and Abundance of Three Key Zooplankters in the Upper San Francisco Estuary

Mon, 28 Aug 2023 00:00:00 +0000

Zooplankton provide critical food for threatened and endangered fish species in the San Francisco Estuary (estuary). Reduced food supply has been implicated in the Pelagic Organism Decline of the early 2000s, and further changes in zooplankton abundance, seasonality, and distribution may continue to threaten declining fishes. While we have a wealth of monitoring data, we know little about the abundance trends of many estuary zooplankton species. To fill these gaps, we reviewed past research and then examined trends in seasonality and abundance from 1972 to the present of three key but understudied zooplankton species (Bosmina longirostris, Acanthocyclops spp., and Acartiella sinensis) that play important roles in the estuary food web. We fit Bayesian generalized additive mixed models of each taxon’s relationship with salinity, seasonality, year, and geography on an integrated database of zooplankton monitoring in the upper estuary. We found marked changes...

An Approach to Defining a Sacramento River Fall Chinook Escapement Objective Considering Natural Production, Hatcheries, and Risk Tolerance

Mon, 28 Aug 2023 00:00:00 +0000

The escapement objective used to manage fisheries for Sacramento River Fall Chinook (SRFC) Salmon was established in 1984. Despite substantial changes to the system and multiple calls to re-evaluate the objective, data and analytical limitations have slowed progress. Synthesizing the available information is further complicated by the different measurement scales employed by relevant studies. Here, I offer a modeling framework for integrating consideration of established hatchery spawning goals, natural-area production or habitat capacities measured at varying spatial scales, and policy decisions about what fraction of potential natural production is desired along with risk tolerance. The model allows evaluating how likely a potential escapement goal (measured at the currently-used scale of fall-run adults returning to both hatcheries and natural areas throughout the Sacramento River basin) is both to meet hatchery goals and to produce at least a specified fraction of potential...

Habitat Use by Breeding Waterbirds in Relation to Tidal Marsh Restoration in the San Francisco Bay Estuary

Thu, 8 Jun 2023 00:00:00 +0000

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...

A Note on Conservative Mixing: Implications for Selecting Salinity-Transport Model Constituents in the San Francisco Estuary

Thu, 8 Jun 2023 00:00:00 +0000

The deviation of specific electrical conductance (EC) from conservative mixing behavior is well-established in the scientific literature. This principle is based on the observation that, as salt concentration in a water sample increases, the mobility of individual ions in the sample decreases, and thus their ability to conduct electricity decreases. Despite this fact, some commonly used models for salinity transport in the San Francisco Estuary (estuary) utilize EC as a primary simulation constituent, treating it as a conservative quantity. Such a modeling approach has likely been followed to exploit the wide availability of EC data for model calibration and validation, and to obviate the need to translate between EC and salinity in a domain characterized by multiple source waters with varying ionic make-ups. Arguably, this approach provides a reasonable trade-off between data translation error and model simulation error. In this paper, we critically evaluate this approach, employing...

Flow Augmentations Modify an Estuarine Prey Field

Thu, 8 Jun 2023 00:00:00 +0000

Zooplankton density and community composition in estuaries can be affected by variation in freshwater inputs, with important implications for higher trophic levels. In the San Francisco Estuary, management agencies have initiated autumn flow augmentations in the form of changes to reservoir releases or to exported water from the South Delta to increase and improve available habitat for endangered Delta Smelt, Hypomesus transpacificus, during the season when their body condition most influences fecundity. Autumn flow augmentation only occurs in years with higher precipitation, effectively moving the Low-Salinity Zone (LSZ) downstream to key foraging habitats for Delta Smelt in Suisun Bay and Suisun Marsh. To assess whether augmented flow enhanced prey resources for Delta Smelt, we compared autumn zooplankton abundance, biomass, spatial distribution, and community composition in years when flow was augmented (2017, 2019) with reference years when flow was not augmented...

What Controls Suspended-Sediment Concentration and Export in Flooded Agricultural Tracts in the Sacramento–San Joaquin Delta?

Tue, 21 Mar 2023 00:00:00 +0000

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...

The Flood Risk and Water Supply Implications of Seasonal Precipitation Reconstructions in Northern California

Tue, 21 Mar 2023 00:00:00 +0000

Subsets of annual and sub-annual tree-ring chronologies are used to reconstruct seasonal precipitation totals in northern California. The specific seasons selected for reconstruction are based on the strongest monthly precipitation signals recorded in the tree-ring data. Earlywood width of gray pine is best correlated with Oct-Dec precipitation at the onset of the wet season. Latewood width of ponderosa pine is correlated with Mar–Apr totals at the end of the wet season. These earlywood and latewood width chronologies are used to develop separate reconstructions of precipitation for the “autumn” (Oct–Dec) and “spring” (Mar–Apr) seasons. Total ring-width chronologies of blue oak are highly correlated with October–April precipitation totals and are used to reconstruct precipitation for the “wet season.” We then computed one additional skillful reconstruction by subtracting the reconstructed spring totals from the wet season precipitation estimates (i.e., “winter” [Oct–Feb]). We...

Data to Decisions: How to Make Science More Relevant for Management of the San Francisco Estuary

Tue, 21 Mar 2023 00:00:00 +0000

Science is the foundation for a wide range of activities, including evaluation, innovation, and technology, which in turn support management. Without good science, resource management in regions such as the San Francisco Estuary is handicapped, and must proceed with outdated conceptual models, operating strategies, and technologies. At the same time, we recognize that poor communication can interfere with conversations between scientists and managers, even when high-quality data and publications are available. In this essay, we have tried to address an important part of this issue: helping scientists to understand how to produce actionable science. Our hope is that these suggestions will, at the least, help improve dialog between scientists and the managers responsible for the estuary’s resources.

Investigating Factors Contributing to Phytoplankton Biomass Declines in the Lower Sacramento River

Tue, 21 Mar 2023 00:00:00 +0000

Phytoplankton subsidies from river inputs and wetland habitats can be important food sources for pelagic organisms in the Sacramento–San Joaquin Delta (Delta). However, while the Sacramento River is a key contributor of water to the Delta, providing 80% of the mean annual inflow, the river is only a minor source of phytoplankton to the system. The reason for low phytoplankton biomass in the Sacramento River is not well understood but appears to be associated with a 65-km stretch of the lower river where chlorophyll-a (Chl-a) concentrations can decline by as much as 90%. We conducted two surveys along the lower Sacramento River, in spring and fall of 2016, to investigate the relative contributions of different factors potentially driving this Chl-a decline. Our study evaluated the change in Chl-a concentrations as a result of dilution from tributaries, light availability, nutrient concentrations, nutrient uptake, phytoplankton productivity, zooplankton grazing, and clam grazing....

Remote Sensing of Primary Producers in the Bay–Delta

Thu, 2 Feb 2023 00:00:00 +0000

Remote-sensing methods are being used to study a growing number of issues in the San Francisco Estuary, such as (1) detecting the optical properties of chlorophyll-a concentrations and dissolved organic matter to assess productivity and the nature of carbon inputs, (2) creating historical records of invasive aquatic vegetation expansion through space and time, (3) identifying origins and expansions of invasions, and (4) supporting models of greenhouse-gas sequestration by expanding restoration projects. Technological capabilities of remote sensing have likewise expanded to include a wide array of opportunities: from boat-mounted sensors, human-operated low-flying planes, and aerial drones, to freely accessible satellite imagery. Growing interest in coordinating these monitoring methods in the name of collaboration and cost-efficiency has led to the creation of diverse expert teams such as the Remote Imagery Collaborative, and monitoring frameworks such as the Interagency...

Carbon Sequestration and Subsidence Reversal in the Sacramento–San Joaquin Delta and Suisun Bay: Management Opportunities for Climate Mitigation and Adaptation

Wed, 1 Feb 2023 00:00:00 +0000

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,...

Landscape Transformation and Variation in Invasive Species Abundance Drive Change in Primary Production of Aquatic Vegetation in the Sacramento–San Joaquin Delta

Wed, 1 Feb 2023 00:00:00 +0000

Conversion of wetlands in the Sacramento–San Joaquin Delta beginning in the mid-1800s resulted in a pronounced shift from a wetland-dominated food web to one driven by open-water primary producers. Submersed and floating aquatic vegetation (SAV and FAV) now rank highest in potential net primary production (NPP) among producer groups, and provide a comparable amount of carbon to the detrital food web as marshes. However, important details of this contribution that relate to shifts in species composition and habitat extent were not understood. Here, we review how changes in aquatic vegetation influence NPP and trophic support from the historical to modern periods, within the modern period (the last 2 decades), and under future management and climate scenarios. We estimate that NPP of SAV and FAV during the historical period was approximately half that of today, before increases in open water and introduction of the highly productive water primrose. During the modern period (the...

Ecology and Ecosystem Effects of Submerged and Floating Aquatic Vegetation in the Sacramento–San Joaquin Delta

Wed, 1 Feb 2023 00:00:00 +0000

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,...

Invasive Aquatic Vegetation in the Sacramento–San Joaquin Delta and Suisun Marsh: The History and Science of Control Efforts and Recommendations for the Path Forward

Wed, 1 Feb 2023 00:00:00 +0000

Invasive aquatic vegetation (IAV) is a management challenge in the Sacramento–San Joaquin Delta and the Suisun Marsh that has commanded major resource investment for 4 decades. We review the history and supporting science of chemical, biological, and mechanical control of IAV in the Delta and Suisun March, and in flowing waters outside the region. Outside the Delta, there is a significant history of research on IAV control in lotic systems, but few studies come from tidal environments, and we found no investigations at a spatial scale like that of the Delta. The science of control efforts in the Delta is nascent but has seen marked growth over the recent decade. Since 1983, control of invasive submerged and floating species has been centralized within the California State Parks Division of Boating and Waterways (CDBW). The program relies on herbicides, with an annual budget that has exceeded $12.5 million since 2015. However, the results have been mixed because of the challenge...

Status, Trends, and Drivers of Harmful Algal Blooms Along the Freshwater-to-Marine Gradient in the San Francisco Bay–Delta System

Wed, 1 Feb 2023 00:00:00 +0000

Harmful algal blooms (HABs) are on the rise worldwide. Known drivers for the proliferation and intensification of HAB events include increasing nutrient pollution, climate change, regulation and modification of hydrological flow, and the combined effect of climate drivers and nutrient pollution. The San Francisco Bay–Delta system has largely been immune to severe or acute HAB events, but there is both a potential and realized threat which has been underestimated and under-reported, in part because of the lack of coordinated sampling and data reporting. There is also increasing evidence that HABs must be considered in the context of a freshwater-to-marine continuum, and that the physical and political boundaries separating components of the Bay–Delta system are porous barriers to HABs and their toxins. Much remains to be learned about the ecology and physiology of HAB organisms in this system, but five primary environmental drivers can be identified: temperature, salinity, irradiance,...

Ecosystem Services and Disservices of Bay-Delta Primary Producers: How Plants and Algae Affect Ecosystems and Respond to Management of the Estuary and Its Watershed

Wed, 25 Jan 2023 00:00:00 +0000

The Sacramento–San Joaquin Delta (Delta) is a case-study of the Anthropocene “great accelerations,” with exponentially increasing temperatures and sea level over time, leading to rapid change in other ecosystem components. In nearly all these interconnected changes and across scales, primary producers play a major role, with diverse effects that mitigate or exacerbate the rapid change induced by climate or other human-driven perturbations. Through this anthropocentric lens, primary producers can be viewed as performing numerous ecosystem services—which ultimately benefit humans—as well as ecosystem disservices, which negatively affect human communities. For example, through carbon sequestration, wetlands can perform ecosystem services of mitigating warming at a global scale and combating relative sea-level rise at a local scale, while generating food that supports regional food webs and fisheries. On the other hand, invasive aquatic vegetation (IAV) can trap sediment before it...

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

Tue, 11 Oct 2022 00:00:00 +0000

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...

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

Tue, 11 Oct 2022 00:00:00 +0000

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...

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

Tue, 11 Oct 2022 00:00:00 +0000

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...

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

Tue, 11 Oct 2022 00:00:00 +0000

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,...

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

Tue, 11 Oct 2022 00:00:00 +0000

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...

Nutrient and Trace Element Contributions from Drained Islands in the Sacramento–San Joaquin Delta, California

Mon, 20 Jun 2022 00:00:00 +0000

Inventorying nutrient and trace element sources in the Sacramento-San Joaquin Delta (the Delta) is critical to understanding how changes—including alterations to point source inputs such as upgrades to the Sacramento Regional Wastewater Treatment Plant (SRWTP) and landscape-scale changes related to wetland restoration—may alter the Delta’s water quality. While island drains are a ubiquitous feature of the Delta, limited data exist to evaluate island drainage mass fluxes in this system. To better constrain inputs from island drains, we measured monthly discharge along with nutrient and trace element concentrations in island drainage on three Delta islands and surrounding rivers from June 2017 to September 2018. These data were used to calculate island-level fluxes and then upscaled to estimate Delta-wide contributions from island drains. Based on these results, we present (1) new estimates of gross and net nutrient and trace element fluxes from Delta island drains, and (2) concomitant...

Considerations for the Development of a Juvenile Production Estimate for Central Valley Spring-Run Chinook Salmon

Mon, 20 Jun 2022 00:00:00 +0000

Effective species management depends on accurate estimates of population size. There are, however, no estimates of annual juvenile production for Central Valley spring-run Chinook Salmon (“spring run”), a highly imperiled species in California, making it difficult to evaluate population status and effectively manage key issues such as entrainment of this species at water diversions. In recognition of this critical information gap, we initiated an effort to develop a juvenile production estimate (JPE) for spring run, defined here as an annual forecast of the number of juvenile Central Valley spring-run Chinook Salmon that enter the Sacramento–San Joaquin Delta (“Delta”) from the Sacramento Valley. This metric would allow for a more robust scientific assessment of the population, which is needed to effectively manage water to reduce effects on spring run, a key condition of state permit requirements. To help guide this effort, we organized a workshop for stake-holders, managers,...

Gill Net Selectivity for Fifteen Fish Species of the Upper San Francisco Estuary

Mon, 20 Jun 2022 00:00:00 +0000

Gill-net size selectivity for fifteen fish species occurring in the upper San Francisco Estuary was estimated from a data set compiled from multiple studies which together contained 7,096 individual fish observations from 882 gill net sets. The gill nets considered in this study closely resembled the American Fisheries Society’s recommended standardized experimental gill nets for sampling inland waters. Relationships between gill-net mesh sizes and the sizes for each fish species retained in them were estimated indirectly using generalized linear modeling and maximum likelihood. Selectivity curves are provided for each species to inform researchers about population characteristics of fishes sampled with similar gill nets.

Climate Change Impacts on San Francisco Estuary Aquatic Ecosystems: A Review

Mon, 20 Jun 2022 00:00:00 +0000

Climate change is intensifying the effects of multiple interacting stressors on aquatic ecosystems worldwide. In the San Francisco Estuary, signals of climate change are apparent in the long-term monitoring record. Here we synthesize current and potential future climate change effects on three main ecosystems (floodplain, tidal marsh, and open water) in the upper estuary and two representative native fishes that commonly occur in these ecosystems: anadromous Chinook Salmon (Oncorhynchus tshawytscha) and estuarine resident Sacramento Splittail, (Pogonichthys macrolepidotus). Based on our review, we found that the estuary is experiencing shifting baseline environmental conditions, amplification of extremes, and restructuring of physical habitats and biological communities. We present priority topics for research and monitoring, and a conceptual model of how the estuary currently functions in relation to climate variables. In addition, we discuss four tools for...

Machine Learning Forecasts to Reduce Risk of Entrainment Loss of Endangered Salmonids at Large-Scale Water Diversions in the Sacramento–San Joaquin Delta, California

Mon, 20 Jun 2022 00:00:00 +0000

Incidental entrainment of fishes at large-scale state and federal water diversion facilities in the Sacramento-San Joaquin Delta, California, can trigger protective management actions when limits imposed by environmental regulations are approached or exceeded. These actions can result in substantial economic costs, and likewise they can affect the status of vulnerable species. Here, we examine data relevant to water management actions during January–June; the period when juvenile salmonids are present in the Delta. We use a quantile regression forest approach to create a risk forecasting tool, which can inform adjustments of diversions based on near real-time predictions. Models were trained using historical entrainment data (Water Years 1999–2019) for Sacramento River winter-run Chinook Salmon or Central Valley Steelhead and a suite of environmental and water operations metrics. A range of models was developed; their performance was evaluated by comparison of a quantile loss...

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

Sun, 6 Mar 2022 00:00:00 +0000

Organic matter in soils and sediments derives from a mixture of biological origins, often making it difficult to determine inputs from individual sources. Complicating the determination of source inputs to soil and sedimentary organic matter (OM) is the fact that physical and microbial processes have likely modified the initial composition of these sources. This study focused on identifying the composition of watershed-derived OM to better understand inputs to inland waters and improve our ability to resolve between terrigenous and aquatic sources in downstream systems, such as estuaries and coasts. We surveyed OM sources from the Yuba River watershed in northern California to identify specific biomarkers that represent aquatic and terrigenous OM sources. Multiple classes of organic proxies—including sterols, fatty acids (FA), lignin phenols and stable carbon and nitrogen isotope values (δ¹³C, δ¹⁵N)—were measured in soils, vegetation, charcoal, and freshwater...

Investigation of Molecular Pathogen Screening Assays for Use in Delta Smelt

Sun, 6 Mar 2022 00:00:00 +0000

Pathogen surveillance must be part of any population supplementation or reintroduction program for the conservation of threatened and endangered species. The unintended transmission of pathogens can have devastating effects on these already at-risk populations or the natural ecosystem at large. In the San Francisco Estuary (estuary), abundance of the endemic Delta Smelt (Hypomesus transpacificus) has declined to the point where regulatory managers are preparing to augment the wild population using fish propagated in a hatchery to prevent species extinction. Although disease is not an overt cause of population decline, comprehensive pathogen presence and prevalence data are lacking. Here, we performed 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. We found the assays to...

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

Sun, 6 Mar 2022 00:00:00 +0000

Fish monitoring gears rarely capture all available fish, an inherent bias in monitoring programs referred to as catchability. Catchability is a source of bias that can be affected by numerous aspects of gear deployment (e.g., deployment speed, mesh size, and avoidance behavior). Thus, care must be taken when multiple surveys—especially those using different sampling methods—are combined to answer spatio-temporal questions about population and community dynamics. We assessed relative catchability differences among four long-term fish monitoring surveys from the San Francisco Estuary: the Bay Study Otter Trawl (BSOT), the Bay Study Midwater Trawl (BSMT), the Fall Midwater Trawl (FMWT), and the Suisun Marsh Otter Trawl (SMOT). We used generalized additive models with a spatio-temporal smoother and survey as a fixed effect to predict gear-specific estimates of catch for 45 different fish species within large and small size classes. We used estimates of the fixed effect coefficients...

Variation in Juvenile Salmon Growth Opportunities Across a Shifting Habitat Mosaic

Sun, 6 Mar 2022 00:00:00 +0000

Historically, Chinook Salmon in the California Central Valley reared in the vast wetlands of the Sacramento–San Joaquin Delta. However, more than 95% of floodplain, riparian, and wetland habitats in the Delta have become degraded because of anthropogenic factors such as pollution, introduced species, water diversions, and levees. Despite pronounced habitat loss, previous work using otolith reconstructions has revealed that some juvenile salmon continue to successfully rear for extended periods in the Delta. However, the extent to which the Delta functions to promote salmon growth relative to other habitats remains unknown. In this study, we integrated otolith microstructure (daily increment count and width) and strontium isotope (87Sr/86Sr) records to fill this critical knowledge gap by comparing the growth of natural-origin fall-run Chinook Salmon from the American River that reared in the Delta with those that remained in their natal stream. Using generalized additive models,...

Counting the Parts to Understand the Whole: Rethinking Monitoring of Steelhead in California’s Central Valley

Sun, 6 Mar 2022 00:00:00 +0000

Steelhead (Oncorhynchus mykiss expressing an anadromous life history) in the Sacramento and San Joaquin rivers and their tributaries in California’s Central Valley (CCV) belong to a Distinct Population Segment (DPS) that is listed as threatened under the US Endangered Species Act. Although contemporary management and recovery plans include numerous planned and ongoing efforts seeking to aid in DPS recovery—such as gravel augmentation, manipulation of spring flows, and restoration of rearing and spawning habitat—a paucity of data precludes the possibility of evaluating the effect of these actions on populations of Steelhead in CCV streams. Knowledge gaps relating to historic and current abundance, population-specific ratios of resident and anadromous life-history expression, and the influence of hatchery-reared fish remain largely unaddressed. This is partly a result of aspects of Steelhead biology that make them difficult to monitor, including the multitude of factors...

Concentrations, Loads, and Associated Trends of Nutrients Entering the Sacramento–San Joaquin Delta, California