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At least 55 records · Page 3Linked to original sources
USGS2016

Climate change and the Delta

Anthropogenic climate change amounts to a rapidly approaching, “new” stressor in the Sacramento–San Joaquin Delta system. In response to California’s extreme natural hydroclimatic variability, complex water-management systems have been developed, even as the Delta’s natural ecosystems have been largely devastated. Climate change is projected to challenge these management and ecological systems in different ways that are characterized by different levels of uncertainty. For example, there is high certainty that climate will warm by about 2°C more (than late-20th-century averages) by mid-century and about 4°C by end of century, if greenhouse-gas emissions continue their current rates of acceleration. Future precipitation changes are much less certain, with as many climate models projecting wetter conditions as drier. However, the same projections agree that precipitation will be more intense when storms do arrive, even as more dry days will separate storms. Warmer temperatures will likely enhance evaporative demands and raise water temperatures. Consequently, climate change is projected to yield both more extreme flood risks and greater drought risks. Sea level rise (SLR) during the 20th century was about 22cm, and is projected to increase by at least 3-fold this century. SLR together with land subsidence threatens the Delta with greater vulnerabilities to inundation and salinity intrusion. Effects on the Delta ecosystem that are traceable to warming include SLR, reduced snowpack, earlier snowmelt and larger storm-driven streamflows, warmer and longer summers, warmer summer water temperatures, and water-quality changes. These changes and their uncertainties will challenge the operations of water projects and uses throughout the Delta’s watershed and delivery areas. Although the effects of climate change on Delta ecosystems may be profound, the end results are difficult to predict, except that native species will fare worse than invaders. Successful preparation for the coming changes will require greater integration of monitoring, modeling, and decision making across time, variables, and space than has been historically normal.

San Francisco Estuary and Watershed Science↗
USGS2016

Nutrient dynamics of the Delta: Effects on primary producers

Increasing clarity of Delta waters, the emergence of harmful algal blooms, the proliferation of aquatic water weeds, and the altered food web of the Delta have brought nutrient dynamics to the forefront. This paper focuses on the sources of nutrients, the transformation and uptake of nutrients, and the links of nutrients to primary producers. The largest loads of nutrients to the Delta come from the Sacramento River with the San Joaquin River seasonally important, especially in the summer. Nutrient concentrations reflect riverine inputs in winter and internal biological processes during periods of lower flow with internal nitrogen losses within the Delta estimated at approximately 30% annually. Light regime, grazing pressure, and nutrient availability influence rates of primary production at different times and locations within the Delta. The roles of the chemical form of dissolved inorganic nitrogen in growth rates of primary producers in the Delta and the structure of the open-water algal community are currently topics of much interest and considerable debate. Harmful algal blooms have been noted since the late 1990s, and the extent of invasive aquatic macrophytes (both submerged and free-floating forms) has increased especially during years of drought. Elevated nutrient loads must be considered in terms of their ability to support this excess biomass. Modern sensor technology and networks are now deployed that make high-frequency measurements of nitrate, ammonium, and phosphate. Data from such instruments allow a much more detailed assessment of the spatial and temporal dynamics of nutrients. Four fruitful directions for future research include utilizing continuous sensor data to estimate rates of primary production and ecosystem respiration, linking hydrodynamic models of the Delta with the transport and fate of dissolved nutrients, studying nutrient dynamics in various habitat types, and exploring the use of stable isotopes to trace the movement and fate of effluent-derived nutrients.

California↗
USGS2018

Toward salt marsh harvest mouse recovery: A review

The salt marsh harvest mouse (SMHM, Reithrodontomys raviventris ) is an endangered species, endemic to the San Francisco Estuary. Despite being protected for almost half a century and being included in a large number of recovery, restoration, and management plans, significant data gaps hinder conservation and management of the species, a challenge further complicated by developing threats such as climate change. In this review, we present the current state of knowledge; highlight research gaps on habitat requirements and distribution, taxonomic status and genetic structure, physiology, reproduction and demographics, population dynamics, and behavior and community interactions; and present an overview of threats to the species. Our review indicates that substantial data gaps exist; although some aspects of SMHM ecology, such as habitat use, have been addressed extensively, others, such as the effects of environmental contamination, are largely unaddressed. We suggest that conservation and restoration-planning processes consider experimental approaches within restoration designs to address these deficiencies. Continued investment in basic and applied SMHM ecology to collect baseline and long-term data will also be beneficial. Additionally, further coordination among managers and researchers can facilitate more effective responses to uncertainties and emerging threats, especially climate change, which threatens the SMHM and its habitat throughout its range.

San Francisco Estuary and Watershed Science↗
USGS2018

Zooplankton dynamics in the Cache Slough complex of the upper San Francisco Estuary

We studied abundance and dynamics of zooplankton in the tidal freshwater Cache Slough Complex (CSC) in the northern Delta of the San Francisco Estuary during June, July, and October 2015. We asked whether the CSC was an area of high zooplankton production that could act as a source region for open waters of the estuary. Abundance of the copepod Pseudodiaptomus forbesi was similar to that in freshwater reaches of the central and eastern Delta and higher than that in the adjacent Sacramento River. Growth rate of P. forbesi was higher than previously measured in large estuarine channels because of higher temperature and phytoplankton biomass in the CSC. Samples of P. forbesi examined with molecular techniques contained an unexpectedly high proportion of DNA from cyanobacteria and little DNA from more nutritious phytoplankton. We also examined tidal exchanges of phytoplankton biomass and copepods between Liberty Island, a shallow tidal lake within the CSC, and the adjacent southern Cache Slough, which links the CSC to the Sacramento River. We calculated zero net flux of phytoplankton over 127 days between June and October. The tidal flux of copepods, calculated using tidal flow from an in situ flow station and half-hourly sampling over three 24.8-hr tidal cycles, varied a great deal because of temporal patchiness and day/night variation in abundance. Overall, the tidal flux was indistinguishable from zero, while the tidally-averaged water flow (and therefore the net copepod flux) was always into the wetland. Our results show some promise for the CSC as a productive habitat for planktivorous fishes and as a laboratory for learning how to design future wetland restoration. However, we remain cautious about whether wetlands such as the CSC may export large quantities of food organisms that can support fishes in other regions of the estuary.

San Francisco Estuary and Watershed Science↗
USGS2018

Hourly analyses of the large storms and atmospheric rivers that provide most of California's precipitation in only 10 to 100 hours per year

California is regularly impacted by floods and droughts, primarily as a result of too many or too few atmospheric rivers (ARs). This study analyzes a two-decade-long hourly precipitation dataset from 176 California weather stations and a 3-hourly AR chronology to report variations in rainfall events across California and their association with ARs. On average, 10-40 and 60-120 hours of rainfall in southern and northern California, respectively, are responsible for more than half of annual rainfall accumulations. Approximately 10-30% of annual precipitation at locations across the state is from only one large storm. On average, northern California receives 25-45 rainfall events annually (40-50% of which are AR-related). These events typically have longer durations and higher event-precipitation totals than those in southern California. Northern California also receives more AR landfalls with longer durations and stronger Integrated Vapor Transport (IVT). On average, ARs contribute 79%, 76%, and 68% of extreme-rainfall accumulations (i.e., top 5% events annually) in the north coast, northern Sierra, and Transverse Ranges of southern California, respectively. The San Francisco Bay Area terrain gap in the California Coast Range allows more AR water vapor to reach inland over the Delta and Sacramento Valley, and thus, influences precipitation in the Delta’s catchment. This is particularly important for extreme precipitation in the northern Sierra Nevada, including river basins above Oroville Dam and Shasta Dam. This study highlights differences between rainfall and AR characteristics in coastal versus inland northern California, differences that largely determine the regional geography of flood risks and water-reliability. These analyses support water resource, flood, levee, wetland, and ecosystem management within the catchment of the San Francisco estuary system by describing regional characteristics of ARs and their influence on rainfall on an hourly timescale.

California↗
USGS2018

An evaluation of three fish surveys in the San Francisco Estuary, 1995–2015

Resource managers rely on long-term monitoring surveys conducted in the San Francisco Estuary to evaluate the status and trends of resident fish populations in this important region. These surveys are potentially confounded because of the incomplete detection of individuals and species, the magnitude of which is often related to the same factors that affect fish populations. We used multistate occupancy estimators to evaluate the distribution, abundance, and detection probability of four fish species collected during 1995–2015 with three long-term surveys. Detection probabilities varied positively with fish abundance and negatively with Secchi depth. Detection varied among species and was greatest for the 20-mm Survey and least for the midwater trawl used for the midwater trawl used in the San Francisco Bay Study. Incomplete detection resulted in underestimates of occupancy and abundance across species and surveys and were greatest for the Bay Study. However, trends in occupancy and abundance of the study period appeared to be unbiased. Fish occupancy and abundance were generally related to salinity or specific conductance, day-of-the year, and water temperature, but the nature of the relations varied among surveys and species. There also was strong spatial and temporal dependence in species-specific occupancy and abundance that changed through time and were unrelated to the covariates considered. Our results suggest that managers consider incorporating methods for estimating detection and adjusting data to ensure data quality. Additionally, the strong spatio-temporal patterns in the monitoring data suggest that existing protocols may need to be modified to ensure that data and inferences reflect system-wide changes rather than changes at a specific set of non-randomly selected locations.

California↗
USGS2019

Chemically enhanced treatment wetland to improve water quality and mitigate land subsidence in the Sacramento-San Joaquin Delta: Cost and design considerations

Water quality impairment and land surface subsidence threaten the viability of the Sacramento-San Joaquin Delta (Delta), a critical component of California’s water conveyance system. Current day irrigation drainage through Delta island peat soils impacts drinking water treatment and is linked to mercury transport, potentially posing both ecological and public health concerns. Hybrid coagulation-treatment wetland systems, termed Chemically Enhanced Treatment Wetlands (CETWs), were studied as a means to cost-effectively treat agricultural drainage water from subsided Delta islands to reduce the export of drinking water quality constituents of concern and mitigate land subsidence through accretion. We provide cost estimates and design recommendations to aid broader implementation of this technology. Over a 20-year horizon using a Total Annualized Cost analysis, we estimate treatment costs of $602 – $747 per acre-foot (ac-ft) water treated and $36 – $70 per kg dissolved organic carbon (DOC) removed depending upon source water DOC concentrations for a small 3-acre CETW system. For larger CETW systems scaled for island sizes of 3,500 – 14,000 acres, costs decrease to $108 – $239 per ac-ft water treated and $11 – $14 per kg DOC removed. The footprints of CETW systems were estimated to be approximately 3% of the area being treated for 4-day hydraulic retention time systems but would decrease to less than 1% for 1-day hydraulic retention time systems. CETWs ultimately address several of the Delta’s key internal issues while keeping water treatment costs competitive with other currently available treatment technologies at similar scales on a per carbon removed basis. CETWs offer a reliable system to reduce out-going DOC and mercury loads and they provide the additional benefit of sediment accretion. System costs and treatment efficacy are highly dependent on inflow source water conditions, land availability and other practical matters. To keep costs low and removal efficacy high, wetland design features will need site-specific evaluation.

California↗
USGS2019

Movement and apparent survival of acoustically tagged juvenile late-fall run chinook salmon released upstream of Shasta Reservoir, California

Stakeholder interests have spurred the reintroduction of the critically endangered populations of Chinook Salmon to tributaries upstream of Shasta Dam, in northern California. We released two groups of acoustically tagged, juvenile hatchery, late-fall Chinook Salmon to determine how juvenile salmon would distribute and survive. We measured travel times to Shasta Dam, and the number of fish that moved between locations within Shasta Reservoir. We used mark-recapture methods to determine detection and apparent survival probabilities of the tagged fish as they traveled through five reaches of the Sacramento River from the McCloud River to San Francisco Bay (~590 km) over the two 3-month observation periods. After our first (February) release of 262 tagged fish, 182 fish (70%) were detected at least once at the dam, 41 (16%) were detected at least once downstream of Shasta Dam, and 3 (1%) traveled as far as San Francisco Bay. After the second (November) release of 355 tagged fish, only 4 (1%) were detected at Shasta Dam. No fish were detected below Shasta Dam, so we could not estimate survival for this second release group. The first release of fish was fortuitously exposed to exceptionally high river flows and dam discharges, which may have contributed to the more distant downstream migration and detection of these fish — though other factors such as season, diploid versus triploid, and fish maturation and size may have also contributed to release differences. The reported fish travel times as well as detection and survival rates are the first estimates of juvenile salmon emigration from locations above Shasta Dam in more than 70 years. This information should help inform resource managers about how best to assess juvenile winter-run Chinook Salmon and assist in their reintroduction to watersheds upstream of Shasta Dam.

California↗
USGS2019

Review of and recommendations for monitoring contaminants and their effects in the San Francisco Bay−Delta

Legacy and current-use contaminants enter into and accumulate throughout the San Francisco Bay−Delta (Bay−Delta), and are present at concentrations with known effects on species important to this diverse watershed. There remains major uncertainty and a lack of focused research able to address and provide understanding of effects across multiple biological scales, despite previous and ongoing emphasis on the need for it. These needs are challenging specifically because of the established regulatory programs that often monitor on a chemical- by-chemical basis, or in which decisions are grounded in lethality-based endpoints. To best address issues of contaminants in the Bay−Delta, monitoring efforts should consider effects of environmentally relevant mixtures and sub- lethal impacts that can affect ecosystem health. These efforts need to consider the complex environment in the Bay−Delta including variable abiotic (e.g., temperature, salinity) and biotic (e.g., pathogens) factors. This calls for controlled and focused research, and the development of a multi-disciplinary contaminant monitoring and assessment program that provides information across biological scales. Information gained in this manner will contribute toward evaluating parameters that could alleviate ecologically detrimental outcomes. This review is a result of a Special Symposium convened at the University of California−Davis (UCD) on January 31, 2017 to address critical information needed on how contaminants affect the Bay−Delta. The UCD Symposium focused on new tools and approaches for assessing multiple stressor effects to freshwater and estuarine systems. Our approach is similar to the recently proposed framework laid out by the U.S. Environmental Protection Agency (USEPA) that uses weight of evidence to scale toxicological responses to chemical contaminants in a laboratory, and to guide the conservation of priority species and habitats. As such, we also aimed to recommend multiple endpoints that could be used to promote a multi-disciplinary understanding of contaminant risks in Bay−Delta while supporting management needs.

California↗
USGS2020

Combining models of the critical streakline and the cross-sectional distribution of juvenile salmon to predict fish routing at river junctions

Because fish that enter the interior Delta have poorer survival than those emigrating via the Sacramento River, understanding the mechanisms that drive entrainment rates at side channel junctions is critically important for the management of imperiled juvenile salmon. Here, we implement a previously proposed process-based conceptual model to study entrainment rates based on three linked elements: the entrainment zone, critical streakline, and cross-sectional distribution of fish. The critical streakline is the location along a channel cross-section immediately upstream of a junction that forms the spatial divide between parcels of water that enter a side channel or remain in the main channel. The critical streakline therefore divides the main channel into entrainment zones within which fish would likely enter each channel. Combined with information about the cross-sectional distribution of fish upstream of a junction, this conceptual model provides a means to predict fish entrainment into each channel. To apply this conceptual model, we combined statistical models of the critical streakline, the cross-sectional distribution of acoustic tagged juvenile Chinook salmon, and their probability of entrainment into Georgiana Slough. We fit joint beta regression and logistic regression models to acoustic telemetry data gathered in 2011 and 2012 to estimate the cross-sectional distribution of fish upstream of the junction, and to estimate the probability of entrainment for fish on either side of the critical streakline. We show that entrainment rates can be predicted by understanding how the combination of critical streakline position and cross-sectional distribution of fish co-vary as a function of environmental covariates. By integrating over individual positions and entrainment fates to arrive at population-level entrain probability in relation to environmental covariates, our model offers managers a simple but powerful tool to evaluate how alternative actions affect migrating fish.

California↗
USGS2020

Ecological effects of climate-driven salinity variation in the San Francisco Estuary: Can we anticipate and manage the coming changes?

Climate change-driven sea level rise and altered precipitation regimes are predicted to alter patterns of salt intrusion within the San Francisco Estuary. A central question is: Can we use existing knowledge and future projections to predict and manage the anticipated ecological impacts? This was the subject of a 2018 symposium entitled “Ecological and Physiological Impacts of Salinization of Aquatic Systems from Human Activities.” The symposium brought together an inter-disciplinary group of scientists and researchers, resource managers, and policy-makers. Here, we summarize and review the presentations and discussions that arose during the symposium. From a historical perspective, salt intrusion has changed substantially over the past 10,000 years as a result of changing climate patterns, with additional shifts from recent anthropogenic effects. Current salinity patterns in the San Francisco Estuary are driven by a suite of hydrodynamic processes within the given contexts of water management and geography. Based on climate projections for the coming century, significant changes are expected in the processes that determine the spatial and temporal patterns of salinity. Given that native species—including fishes such as the Delta Smelt and Sacramento Splittail—track favorable habitats, exhibit physiological acclimation, and can adaptively evolve, we present a framework for assessing their vulnerability to altered salinity in the San Francisco Estuary. We then present a range of regulatory and structural management tools that are available to control patterns of salinity within the San Francisco Estuary. Finally, we identify major research priorities that can help fill critical gaps in our knowledge about future salinity patterns and the consequences of climate change and sea level rise. These research projects will be most effective with strong linkages and communication between scientists and researchers, resource managers, and policy-makers.

California↗
USGS2020

Use of the smeltCam as an efficient fish sampling alternative within the San Francisco Estuary

Resource managers often rely on long-term monitoring surveys to detect trends in biological data. However, no survey gear is 100% efficient, and many sources of bias can be responsible for detecting or not detecting biological trends. The SmeltCam is an imaging apparatus developed as a potential sampling alternative to long-term trawling gear surveys within the San Francisco Estuary, California, to reduce handling stress on sensitive species like the Delta Smelt ( Hypomesus transpacificus ). Although believed to be a reliable alternative to closed cod-end trawling surveys, no formal test of sampling efficiency has been implemented using the SmeltCam. We used a paired deployment of the SmeltCam and a conventional closed cod-end trawl within the Napa River and San Pablo Bay, a Bayesian binomial N -mixture model, and data simulations to determine the sampling efficiency of both deployed gear types to capture a Delta Smelt surrogate (Northern Anchovy, Engraulis mordax ) and to test potential bias in our modeling framework. We found that retention efficiency—a component of detection efficiency that estimates the probability a fish is retained by the gear, conditional on gear contact—was slightly higher using the SmeltCam (mean = 0.58) than the conventional trawl (mean = 0.47, Probability SmeltCam retention efficiency > trawl retention efficiency = 94%). We also found turbidity did not affect the SmeltCam’s retention efficiency, although total fish density during an individual tow improved the trawl’s retention efficiency. Simulations also showed the binomial model was accurate when model assumptions were met. Collectively, our results suggest the SmeltCam to be a reliable alternative to sampling with conventional trawling gear, but future tests are needed to confirm whether the SmeltCam is as reliable when applied to taxa other than Northern Anchovy over a greater range of conditions.

California↗
USGS2021

Breeding waterbird populations have declined in south San Francisco Bay: An assessment over two decades

In south San Francisco Bay, former salt ponds now managed as wildlife habitat support large populations of breeding waterbirds. In 2006, the South Bay Salt Pond Restoration Project began the process of converting 50% to 90% of these managed pond habitats into tidal marsh. We compared American Avocet ( Recurvirostra americana ) and Black-necked Stilt ( Himantopus mexicanus ) abundance in south San Francisco Bay before (2001) and after approximately 1,300 ha of managed ponds were breached to tidal action to begin tidal marsh restoration (2019). Over the 18-year period, American Avocet abundance declined 13.5% (2,765 in 2001 vs. 2,391 in 2019), and Black-necked Stilt abundance declined 30.0% (1,184 in 2001 vs. 828 in 2019). Forster’s Tern ( Sterna forsteri ) abundance was 2,675 birds in 2019. In 2019, managed ponds accounted for only 25.8% of suitable habitats, yet contained 53.9%, 38.6%, and 65.6% American Avocet, Black-necked Stilt, and Forster’s Tern observations, respectively. Conversely, tidal marsh and tidal mudflats accounted for 42.9% of suitable habitats, yet contained only 18.4%, 10.3%, and 19.8% of American Avocet, Black-necked Stilt, and Forster’s Tern observations, respectively. Using a separate nest-monitoring data set, we found that nest abundance in south San Francisco Bay declined for all three species from 2005–2019. Average annual nest abundance during 2017–2019 declined 53%, 71%, and 36%, for American Avocets, Back-necked Stilts, and Forster’s Terns, respectively, compared to 2005–2007. Loss of island nesting habitat as a result of tidal marsh conversion and an increasing population of predatory California Gulls ( Larus californicus ) are two potential causes of these declines. All three species established nesting colonies on newly constructed islands within remaining managed ponds; however, these new colonies did not make up for the steep declines observed at other historical nesting sites. For future wetland restoration, retaining more managed ponds that contain islands suitable for nesting may help to limit further declines in breeding waterbird populations.

California↗
USGS2021

Wetland availability and salinity concentrations for breeding waterfowl in Suisun Marsh, California

Availability of wetlands with low salinities during the breeding season can influence waterfowl reproductive success and population recruitment. Salinities as low as 2 ppt (3.6 mScm–1) can impair duckling growth and influence behavior, with mortality occurring above 9 ppt (14.8 mScm–1). We used satellite imagery to quantify the amount of available water, and sampled surface water salinity at Grizzly Island, in the brackish Suisun Marsh, at three time-periods during waterfowl breeding (April, May, July) over 4 years (2016–2019). More water was available and salinity was lower during wetter years (2017, 2019) than during drier years (2016, 2018), and the amount of water in wetlands decreased 73%–86% from April to July. Across all time-periods and years, the majority (64%–100%) of wetland habitat area had salinities above what has been shown to negatively affect ducklings (> 2 ppt), and up to 42% of wetland area had salinities associated with duckling mortality (> 9 ppt). During peak duckling production in May, 81%–95% of available water had salinity above 2 ppt, and 5%–21% was above 9 ppt. In May of the driest year (2016), only 0.5 km2 of low-salinity water (< 2 ppt) was available to ducklings in the study area, compared to 2.6 km2 in May of the wettest year (2017). Private duck clubs own the majority of wetland habitat at Grizzly Island and consistently had a greater percentage of land flooded during summer than did publicly owned wetlands, but private wetlands generally had higher salinities than public wetlands, likely because they draw from higher-salinity water sources. By July, few wetlands remained flooded, and most had salinities high enough to impair duckling growth and survival. Local waterfowl populations would benefit from management practices that provide fresher water during peak duckling production in May and retain more water through July.

California↗
USGS2021

Dispersion and stratification dynamics in the upper Sacramento River deep water ship channel

Hydrodynamics control the movement of water and material within and among habitats, where time-scales of mixing can exert bottom-up regulatory effects on aquatic ecosystems through their influence on primary production. The San Francisco Estuary (estuary) is a low-productivity ecosystem, which is in part responsible for constraining higher trophic levels, including fishes. Many research and habitat-restoration efforts trying to increase primary production have been conducted, including, as described here, a whole-ecosystem nutrient addition experiment where calcium nitrate was applied in the Sacramento River Deep Water Ship Channel (DWSC) to see if phytoplankton production could be increased and exported out of the DWSC. As an integral part of this experiment, we investigated the physical mechanisms that control mixing, and how these mechanisms affect the strength and duration of thermal stratification, which we revealed as critical for controlling phytoplankton dynamics in the relatively turbid upper DWSC. Analysis of a suite of mixing mechanisms and time-scales show that both tidal currents and wind control mixing rates and stratification dynamics in the DWSC. Longitudinal and vertical dispersion increased during periods of high wind, during which wind speed influenced dispersion more than tidal currents. Thermal stratification developed most days, which slowed vertical mixing but was rapidly broken down by wind-induced mixing. Stratification rarely persisted for longer than 24 hours, limiting phytoplankton production in the study area. The interaction between physical mechanisms that control mixing rates, mediate stratification dynamics, and ultimately limit primary production in the DWSC may be useful in informing habitat restoration elsewhere in the Delta and in other turbid aquatic environments.

California↗
USGS2021

Concentrations, loads, and associated trends of nutrients entering the Sacramento-San Joaquin Delta, California

Statistical modeling of water-quality data collected at the Sacramento River at Freeport and San Joaquin River near Vernalis, California, USA, was used to examine trends in concentrations and loads of various forms of dissolved and particulate nitrogen and phosphorus that entered the Sacramento–San Joaquin River Delta (Delta) from upstream sources between 1970 and 2019. Ammonium concentrations and loads decreased at the Sacramento River site from the mid-1970s through 1990 because of the consolidation of wastewater treatment and continuously reduced from the mid-1970s to 2019 at the San Joaquin River site. Current ammonium concentrations are mostly below 4 µM (0.056 mg N L –1 ) at both sites, a concentration above which reductions in phytoplankton productivity or changes in algal species composition may occur. The Sacramento River at Freeport site is located upstream of the Sacramento Regional County Sanitation District’s treatment facility’s discharge point; nutrient water quality there is representative of upstream sources. Inorganic nitrogen (nitrate plus ammonium) concentrations and loading differed at both sites. At the Sacramento River location, concentrations decrease in the summer agricultural season, reducing the molar ratios of nitrogen to phosphorus. In contrast, inorganic nitrogen concentrations increase in the San Joaquin River during the agricultural season as a result of irrigation runoff, increasing the molar ratio of nitrogen to phosphorus. This increase suggests a possible nitrogen limitation in the northern Delta and a phosphorus limitation in the southern Delta, as indicated by the molar ratios of bioavailable nitrogen to bioavailable phosphorus. Planned upgrades to the Sacramento Regional Wastewater Treatment Plant (SRWTP) will reduce inorganic nitrogen inputs to the northern Delta. Consequently, the supply of bioavailable nitrogen throughout the upper estuary should diminish. Source modeling of nitrogen and phosphorus identifies agriculture, atmospheric deposition, and wastewater effluent as sources of total nitrogen in the Central Valley. In contrast, geologic sources, agriculture, and wastewater discharge are the primary sources of phosphorus.

California↗
USGS2022

Relative bias in catch among long-term fish monitoring surveys within the San Francisco Estuary

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 for each survey (e.g., BSOT) relative to the reference gear (FMWT) to develop relative measures of catchability among taxa, surveys, and fish-size classes, termed the catch-ratio. We found higher relative catchability of 27%, 22%, and 57% of fish species in large size classes from the FMWT than in the BSMT, BSOT, or SMOT, respectively. In the small size class, relative catchability was higher in the FMWT than the BSMT, BSOT, or SMOT for 50%, 18%, and 25% of fish species, respectively. As expected, relative catchability of demersal species was higher in the otter trawls (BSOT, SMOT) while relative catchability of pelagic species was higher in the midwater trawls (FMWT, BSMT). Our results demonstrate that catchability is a source of bias among monitoring efforts within the San Francisco Estuary, and assuming equal catchability among surveys, species, and size classes could result in significant bias when describing spatio-temporal patterns in catch if ignored.

California↗
USGS2022

Gill-net selectivity for fifteen fish species of the upper San Francisco Estuary

Gill-net size selectivity for 15 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.

California↗