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USGS2026

Differences among runs of Chinook Salmon in routing probability at the Georgiana Slough-Sacramento River junction

The survival of juvenile Chinook Salmon ( Oncorhynchus tshawytscha ) depends on the specific migration route they take through the Sacramento–San Joaquin Delta. Factors such as flow magnitude, flow direction, and distribution of fish across the channel significantly affect the likelihood of their entering routes with lower survival probabilities. Management strategies to mitigate the entry of endangered winter-run and threatened spring-run Chinook Salmon into the interior Delta—particularly through Georgiana Slough—involve flow regulation and the installation of a bioacoustic fish fence. Monitoring the effectiveness of these measures has primarily relied on acoustically-tagged, juvenile, hatchery-reared, late-fall-run Chinook Salmon, which are easier to obtain and can accommodate larger tags compared to other runs. Previous studies explored how flow dynamics affect routing probabilities of late-fall-run Chinook Salmon, but there is a lack of understanding about how routing probabilities vary among runs. We leveraged data from 15 previous studies comprising 3,004 acoustically-tagged fish across all four runs, over a 12-year period, to assess the effects of run on routing probability into Georgiana Slough, while accounting for variation in flow dynamics. We employed logistic regression to model the influence of tidal flow metrics, time of day (day and night), and run type on the probability of juvenile Chinook Salmon being routed into Georgiana Slough. Our analysis revealed that reverse flow during incoming tides influenced the routing probabilities of all runs. An increased proportion of flow into Georgiana Slough, meant an increased probability for all runs to be routed into Georgiana Slough. Late-fall-run Chinook Salmon also showed a greater probability of routing into Georgiana Slough during the night than during the day, whereas the opposite was true for other runs. These differences in routing probability affect our understanding of how management actions intended to reduce routing into Georgiana Slough may differentially affect the four runs of Chinook Salmon in the Sacramento River.

Callifornia↗
USGS2010

Mercury-contaminated hydraulic mining debris in San Francisco Bay

The hydraulic gold-mining process used during the California Gold Rush and in many developing countries today contributes enormous amounts of sediment to rivers and streams. Commonly, accompanying this sediment are contaminants such as elemental mercury and cyanide used in the gold extraction process. We show that some of the mercurycontaminated sediment created by hydraulic gold mining in the Sierra Nevada, between 1852 and 1884, ended up over 250 kilometers (km) away in San Francisco Bay; an example of the far-reaching extent of contamination from such activities. A combination of radionuclide dating, bathymetric reconstruction, and geochemical tracers were used to distinguish the hydraulic mining sediment from sediment deposited in the bay before hydraulic mining started (pre-Gold Rush sediment) and sediment deposited after hydraulic mining stopped (modern sediment). Three San Francisco Bay cores were studied as well as source material from the abandoned hydraulic gold mines and river sediment between the mines and bay. Isotopic and geochemical compositions of the core sediments show a geochemical shift in sediment deposited during the time of hydraulic mining. The geochemical shift is characterized by a decrease in εNd, total organic carbon (TOC), Sr and Ca concentrations, Ca/Sr, and Ni/Zr; and, an increase in 87Sr/86Sr, Al/Ca, Hg concentrations, and quartz/plagioclase. This shift is in the direction of the geochemical signature of sediments from rivers and gold mines in hydraulic mining areas. Mixing calculations using Nd isotopes and concentrations estimate that the hydraulic mining debris comprises up to 56% of the sediment in core sediments deposited during the time of hydraulic mining. The surface sediment of cores taken in 1990 were found to contain up to 43% hydraulic mining debris, reflecting a continuing remobilization and redistribution of the debris within the bay and transport from the watershed. Mercury concentrations in pre-Gold Rush sediment range between 0.03 and 0.08 μg g-1. In core sediments that have characteristics of the gold deposits and were deposited during the time of hydraulic mining, mercury concentrations can be up to 0.45 μg/g. Modern sediment (post-1952 deposition) contains mercury concentrations up to 0.79 μg/g and is likely a mix of hydraulic mining mercury and mercury introduced from other sources.

California↗
USGS2006

Flow convergence caused by a salinity minimum in a tidal channel

Residence times of dissolved substances and sedimentation rates in tidal channels are affected by residual (tidally averaged) circulation patterns. One influence on these circulation patterns is the longitudinal density gradient. In most estuaries the longitudinal density gradient typically maintains a constant direction. However, a junction of tidal channels can create a local reversal (change in sign) of the density gradient. This can occur due to a difference in the phase of tidal currents in each channel. In San Francisco Bay, the phasing of the currents at the junction of Mare Island Strait and Carquinez Strait produces a local salinity minimum in Mare Island Strait. At the location of a local salinity minimum the longitudinal density gradient reverses direction. This paper presents four numerical models that were used to investigate the circulation caused by the salinity minimum: (1) A simple one-dimensional (1D) finite difference model demonstrates that a local salinity minimum is advected into Mare Island Strait from the junction with Carquinez Strait during flood tide. (2) A three-dimensional (3D) hydrodynamic finite element model is used to compute the tidally averaged circulation in a channel that contains a salinity minimum (a change in the sign of the longitudinal density gradient) and compares that to a channel that contains a longitudinal density gradient in a constant direction. The tidally averaged circulation produced by the salinity minimum is characterized by converging flow at the bed and diverging flow at the surface, whereas the circulation produced by the constant direction gradient is characterized by converging flow at the bed and downstream surface currents. These velocity fields are used to drive both a particle tracking and a sediment transport model. (3) A particle tracking model demonstrates a 30 percent increase in the residence time of neutrally buoyant particles transported through the salinity minimum, as compared to transport through a constant direction density gradient. (4) A sediment transport model demonstrates increased deposition at the near-bed null point of the salinity minimum, as compared to the constant direction gradient null point. These results are corroborated by historically noted large sedimentation rates and a local maximum of selenium accumulation in clams at the null point in Mare Island Strait.

California↗
USGS2005

From climate-change spaghetti to climate-change distributions for 21st Century California

The uncertainties associated with climate-change projections for California are unlikely to disappear any time soon, and yet important long-term decisions will be needed to accommodate those potential changes. Projection uncertainties have typically been addressed by analysis of a few scenarios, chosen based on availability or to capture the extreme cases among available projections. However, by focusing on more common projections rather than the most extreme projections (using a new resampling method), new insights into current projections emerge: (1) uncertainties associated with future greenhouse-gas emissions are comparable with the differences among climate models, so that neither source of uncertainties should be neglected or underrepresented; (2) twenty-first century temperature projections spread more, overall, than do precipitation scenarios; (3) projections of extremely wet futures for California are true outliers among current projections; and (4) current projections that are warmest tend, overall, to yield a moderately drier California, while the cooler projections yield a somewhat wetter future. The resampling approach applied in this paper also provides a natural opportunity to objectively incorporate measures of model skill and the likelihoods of various emission scenarios into future assessments.

San Francisco Estuary and Watershed Science↗
USGS2008

A note on the effect of wind waves on vertical mixing in Franks Tract, Sacramento-San Joaquin Delta, California, USA

A one-dimensional numerical model that simulates the effects of whitecapping waves was used to investigate the importance of whitecapping waves to vertical mixing at a 3-meter-deep site in Franks Tract in the Sacramento-San Joaquin Delta over an 11-day period. Locally-generated waves of mean period approximately 2 s were generated under strong wind conditions; significant wave heights ranged from 0 to 0.3 m. A surface turbulent kinetic energy flux was used to model whitecapping waves during periods when wind speeds > 5 m s-1 (62% of observations). The surface was modeled as a wind stress log-layer for the remaining 38% of the observations. The model results demonstrated that under moderate wind conditions (5–8 m s-1 at 10 m above water level), and hence moderate wave heights, whitecapping waves provided the dominant source of turbulent kinetic energy to only the top 10% of the water column. Under stronger wind (> 8 m s-1), and hence larger wave conditions, whitecapping waves provided the dominant source of turbulent kinetic energy over a larger portion of the water column; however, this region extended to the bottom half of the water column for only 7% of the observation period. The model results indicated that phytoplankton concentrations close to the bed were unlikely to be affected by the whitecapping of waves, and that the formation of concentration boundary layers due to benthic grazing was unlikely to be disrupted by whitecapping waves. Furthermore, vertical mixing of suspended sediment was unlikely to be affected by whitecapping waves under the conditions experienced during the 11-day experiment. Instead, the bed stress provided by tidal currents was the dominant source of turbulent kinetic energy over the bottom half of the water column for the majority of the 11-day period.

California↗
USGS2006

Variation in spring nearshore resident fish species composition and life histories in the lower San Joaquin watershed and delta

Providing freshwater to human populations while protecting or rehabilitating ecosystem health is a significant challenge to water resource managers and requires accurate knowledge of aquatic resources. Previous studies of fish assemblages in the San Francisco Estuary and watershed have focused on specific habitat types, water bodies, or geographic subregions. In this study, we use seining data from two monitoring programs to provide an integrated view of spring nearshore resident fish species composition and life history characteristics in five regions: the San Joaquin River, the upper Sacramento River, the lower Sacramento River, the northern Sacramento-San Joaquin Delta (North Delta), and the Interior Delta. Data for the period March-May from 1994 to 2002, showed that spring species composition of the San Joaquin River was very different from the other four regions. Total catch in the San Joaquin River was dominated by small, short-lived batch spawning alien species (93%), particularly red shiner Cyprinella lutrensis (>75% of total catch). The upper and lower Sacramento River were very similar in species composition and life history characteristics and less dominated by alien fish (<45% of total catch). Ordination of species percentage abundances by non–metric multidimensional scaling confirmed that the major gradient was from assemblages dominated by native species to assemblages dominated by alien species. Two-way analysis of variance of ordination scores indicated that spatial variability was more important than annual variability in explaining patterns in species composition. The potential benefits of San Joaquin River native fish restoration appear high because there is so much potential for improvement; however, it is unclear how to best manipulate the system to achieve such restoration. Addressing such uncertainties is necessary if society desires the reservation and restoration of native biodiversity as human demands on water resources increase.

California↗
USGS2008

Understanding the occurrence and transport of current-use pesticides in the San Francisco estuary watershed

The occurrence and potential effects of current-use pesticides are of concern in the San Francisco Estuary watershed but our understanding of the spatial and temporal distribution of contamination is limited. This paper summarizes almost two decades of historical data and uses it to describe our current knowledge of the processes controlling the occurrence of current-use pesticides in the watershed. Monitoring studies analyze fewer than half of the pesticides applied in the watershed and most of our knowledge is about inputs of dissolved pesticides in the upper watershed. The four major seasonal patterns of riverine inputs of pesticides to the estuary can be identified by usage and transport mechanism. Dormant spray insecticides applied to orchards and herbicides applied to a variety of crops are transported by rainfall during the winter. Alfalfa pesticides are detected following rainfall and irrigation return flow in the spring, and rice pesticides are detected following release of rice field water in the summer. Irrigation return flows transport a variety of herbicides during the summer. In addition, pesticides applied on Delta islands can cause elevated pesticide concentrations in localized areas. Although not as well characterized, urban creeks appear to have their own patterns of insecticide concentrations causing toxicity throughout most of the year. Current-use pesticides have also been detected on suspended and bed sediments throughout the watershed but limited data make it difficult to determine occurrence patterns. Data gaps include the lack of analysis of many pesticides (or degradates), changing pesticide use, limited information on pesticide transport within the Delta, and an incomplete understanding of the transport and persistence of sediment-associated pesticides. Future monitoring programs should be designed to address these data gaps.

California↗
USGS2008

Subsidence reversal in a re-establish wetland in the Sacramento-San Joaquin Delta, California, USA

The stability of levees in the Sacramento-San Joaquin Delta is threatened by continued subsidence of Delta peat islands. Up to 6 meters of land-surface elevation has been lost in the 150 years since Delta marshes were leveed and drained, primarily from oxidation of peat soils. Flooding subsided peat islands halts peat oxidation by creating anoxic soils, but net accumulation of new material in restored wetlands is required to recover land-surface elevations. We investigated the subsidence reversal potential of two 3 hectare, permanently flooded, impounded wetlands re-established on a deeply subsided field on Twitchell Island. The shallower wetland (design water depth 25 cm) was almost completely colonized by dense emergent marsh vegetation within two years; whereas, the deeper wetland (design water depth 55 cm) which developed spatially variable depths as a result of heterogeneous colonization by emergent vegetation, still had some areas remaining as open water after nine years. Changes in land-surface elevation were quantified using repeated sedimentation-erosion table measurements. New material accumulating in the wetlands was sampled by coring. Land-surface elevations increased by an average of 4 cm/yr in both wetlands from 1997 to 2006; however, the rates at different sites in the wetlands ranged from -0.5 to +9.2 cm/yr. Open water areas of the deeper wetland without emergent vegetation had the lowest rates of land-surface elevation gain. The greatest rates occurred in areas of the deeper wetland most isolated from the river water inlets, with dense stands of emergent marsh vegetation (tules and cattails). Vegetated areas of the deeper wetland in the transition zones between open water and mature emergent stands had intermediate rates of land-surface gain, as did the entire shallower wetland. These results suggest that the dominant component contributing to land-surface elevation gain in these wetlands was accumulation of organic matter, rather than mineral sediment, and that accumulation of organic matter in emergent marshes is strongly affected by hydrologic factors. Re-established, non-tidal wetlands with managed hydrology can produce significant increases in land-surface elevations, which can help to improve levee stability and protect subsided islands from future flooding.

California↗
USGS2008

Principal hydrologic responses to climatic and geologic variability in the Sierra Nevada, California

Sierra Nevada snowpack is a critical water source for California’s growing population and agricultural industry. However, because mountain winters and springs are warming, on average, precipitation as snowfall relative to rain is decreasing, and snowmelt is earlier. The changes are stronger at mid-elevations than at higher elevations. The result is that the water supply provided by snowpack is diminishing. In this paper, we describe principal hydrologic responses to climatic and spatial geologic variations as gleaned from a series of observations including snowpack, stream-flow, and bedrock geology. Our analysis focused on peak (maximum) and base (minimum) daily discharge of the annual snowmelt-driven hydrographs from 18 Sierra Nevada watersheds and 24 stream gage locations using standard correlation methods. Insights into the importance of the relative magnitudes of peak flow and soil water storage led us to develop a hydrologic classification of mountain watersheds based on runoff versus base flow as a percentage of peak flow. Our findings suggest that watersheds with a stronger base flow response store more soil water than watersheds with a stronger peak-flow response. Further, the influence of antecedent wet or dry years is greater in watersheds with high base flow, measured as a percentage of peak flow. The strong correlation between 1) the magnitude of peak flow, and 2) snow water equivalent can be used to predict peak flow weeks in advance. A weaker but similar correlation can be used to predict the magnitude of base flow months in advance. Most of the watersheds show a trend that peak flow is occurring earlier in the year.

California↗
USGS1998

Integrated Natural Resource Science Program, San Francisco Bay

The San Francisco Bay-Delta estuary and its watershed have been a focus of intense human activity and environmental impact since 1848 when gold was discovered in the foothills of California's Sierra Nevada mountains. As the estuary and its watershed continue to be changed by human activities, resource managers, environmental regulators, elected officials, and the public seek credible, unbiased scientific information about the factors related to observed changes in order to restore impaired species, habitats and ecological functions.

California↗
USGS2026

Recent scientific contributions by the U.S. Geological Survey in the San Francisco Bay and Sacramento–San Joaquin Delta Estuary

Introduction The San Francisco Bay and Sacramento–San Joaquin Delta Estuary (hereafter, Bay-Delta) is the largest estuary on the West Coast of the United States. The Bay-Delta covers more than 1,600 square miles and drains a watershed of more than 75,000 square miles, which is greater than 40 percent of California. The region surrounding the Bay-Delta is home to about 10 million people, and its habitats (fig. 1) support more than 800 plant and animal species. The waterways of the Bay-Delta are the central hub of California’s extensive freshwater delivery system, supplying water to more than 27 million Californians and 4 million acres of farmland in the Central Valley. The U.S. Geological Survey (USGS) is the primary science agency of the U.S. Department of the Interior, providing a broad range of Earth, water, biological, and mapping data and expertise to inform natural resource management across the country. This fact sheet focuses on research conducted by the USGS in the Bay-Delta region, mostly within the past 5 years. The fact sheet is organized across five major themes: water flow and water quality, fish and wildlife, wetland restoration, invasive species, and hazards. In each of these areas, the USGS works closely with Federal, State, and local agencies; academia; and non-governmental organizations to provide objective, evidence-based science. The data and knowledge gained from USGS research and monitoring are publicly available and are routinely used by agencies, including the U.S. Bureau of Reclamation, U.S. Army Corps of Engineers, U.S. Fish and Wildlife Service, California Department of Water Resources, California Department of Fish and Wildlife, California State Water Resources Control Board, Delta Stewardship Council, and many additional organizations and stakeholders to inform management of the Bay-Delta region and its resources.

California↗
USGS2007

A cold phase of the East Pacific triggers new phytoplankton blooms in San Francisco Bay

Ecological observations sustained over decades often reveal abrupt changes in biological communities that signal altered ecosystem states. We report a large shift in the biological communities of San Francisco Bay, first detected as increasing phytoplankton biomass and occurrences of new seasonal blooms that began in 1999. This phytoplankton increase is paradoxical because it occurred in an era of decreasing wastewater nutrient inputs and reduced nitrogen and phosphorus concentrations, contrary to the guiding paradigm that algal biomass in estuaries increases in proportion to nutrient inputs from their watersheds. Coincidental changes included sharp declines in the abundance of bivalve mollusks, the key phytoplankton consumers in this estuary, and record high abundances of several bivalve predators: Bay shrimp, English sole, and Dungeness crab. The phytoplankton increase is consistent with a trophic cascade resulting from heightened predation on bivalves and suppression of their filtration control on phytoplankton growth. These community changes in San Francisco Bay across three trophic levels followed a state change in the California Current System characterized by increased upwelling intensity, amplified primary production, and strengthened southerly flows. These diagnostic features of the East Pacific "cold phase" lead to strong recruitment and immigration of juvenile flatfish and crustaceans into estuaries where they feed and develop. This study, built from three decades of observation, reveals a previously unrecognized mechanism of ocean-estuary connectivity. Interdecadal oceanic regime changes can propagate into estuaries, altering their community structure and efficiency of transforming land-derived nutrients into algal biomass.

California↗
USGS2015

High-resolution remote sensing of water quality in the San Francisco Bay-Delta Estuary

The San Francisco Bay&ndash;Delta Estuary watershed is a major source of freshwater for California and a profoundly human-impacted environment. The water quality monitoring that is critical to the management of this important water resource and ecosystem relies primarily on a system of fixed water-quality monitoring stations, but the limited spatial coverage often hinders understanding. Here, we show how the latest technology in visible/near-infrared imaging spectroscopy can facilitate water quality monitoring in this highly dynamic and heterogeneous system by enabling simultaneous depictions of several water quality indicators at very high spatial resolution. The airborne portable remote imaging spectrometer (PRISM) was used to derive high-spatial-resolution (2.6 &times; 2.6 m) distributions of turbidity, and dissolved organic carbon (DOC) and chlorophyll-a concentrations in a wetland-influenced region of this estuary. A filter-passing methylmercury vs DOC relationship was also developed using in situ samples and enabled the high-spatial-resolution depiction of surface methylmercury concentrations in this area. The results illustrate how high-resolution imaging spectroscopy can inform management and policy development in important inland and estuarine water bodies by facilitating the detection of point- and nonpoint-source pollution, and by providing data to help assess the complex impacts of wetland restoration and climate change on water quality and ecosystem productivity.

California↗