Geology topics

Research about San Pablo Bay

Source-linked reports with geographic coverage including San Pablo Bay.

12 recordsLinked to original sources

USGS2023

Observations and morphodynamic modeling of decadal-scale morphologic change in estuaries under sea level rise

Sea level rise is expected to affect coastal areas all around the world, including the estuarine environment. New bathymetry collected in 2014 provided a unique opportunity to test the modeling of Elmilady et al. (2019), who presented a morphodynamic DELFT3D model of San Pablo Bay, California, that included detailed tidal water movement, wind-wave action, sediment transport, and resulting bed level updates. Their hindcasts (1856–1983) showed significant skill in reproducing observed patterns and volumes of deposition and erosion in San Pablo Bay. Their forecasts (1983–2100) showed that sea level rise results in increased deposition, loss of intertidal flats because of drowning, and a greater channel volume. The model, in general, forecasted observed trends in change from 1983 to 2014. Morphodynamic modeling is a promising approach for identifying the effect of sea level rise on estuarine environments.

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USGS2021

Cohesive sediment modeling in a shallow estuary: Model and environmental implications of sediment parameter variation

Numerical models of sediment transport in estuarine systems rely on parameter values that are often poorly constrained and can vary on timescales relevant to model processes. The selection of parameter values can affect the accuracy of model predictions, while environmental variation of these parameters can impact the temporal and spatial ranges of sediment fluxes, erosion, and deposition in the real world. We implemented a numerical model of San Pablo Bay, an embayment within San Francisco Bay, California, for November–December 2014, and compared model outputs to observations of water level, velocity, wave parameters, salinity, and suspended sediment concentration (SSC) in the shallow regions. Idealized model runs show that wind timing relative to the phase of the tides is the strongest control on sediment fluxes and bed erosion. We varied sediment erodibility in the outflow of the Petaluma River; while this causes erosion and deposition to vary strongly through the shallows system, total export from the shallows does not change. Model runs with realistic winds show that wind likely resuspends faster settling particles or allows for more particle flocculation; particle settling velocity controls system-wide sediment accumulation. At the margins of the system, the magnitude of SSC is closely tied to wind direction when winds occur during flood tide, but sediment deposition is less connected: Both bed evolution and SSC need to be considered in the prediction of marsh fate. Spatial patterns of light attenuation due to SSC is strongly tied to assumed settling velocity.

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USGS2021

Assessment of flood forecast products for a coupled tributary-Coastal model

Compound flooding, resulting from a combination of riverine and coastal processes, is a complex but important hazard to resolve along urbanized shorelines in the vicinity of river mouths. However, inland flooding models rarely consider oceanographic conditions, and vice versa for coastal flood models. Here, we describe the development of an operational, integrated coastal-watershed flooding model to address this issue of compound flooding in a highly urbanized estuarine environment, San Francisco Bay (CA, USA), where the surrounding communities are susceptible to flooding along the bay shoreline and inland rivers and creeks that drain to the bay. The integrated tributary-coastal forecast model (Hydro-Coastal Storm Modeling System, or Hydro-CoSMoS) was developed to provide water managers and other users with flood forecast information beyond what is currently available. Results presented here are focused on the interaction of the Napa River watershed and the San Pablo Bay at the northern end of San Francisco Bay. This paper describes the modeling setup, the scenario used in a tabletop exercise (TTE), and the assessment of the various flood forecast information products. Hydro-CoSMoS successfully demonstrated the capability to provide watershed and coastal flood information at scales and locations where no such information is currently available and was also successful in showing how tributary flows could be used to inform the coastal storm model during a flooding scenario. The TTE provided valuable feedback on how to guide continued model development and to inform what model outputs and formats are most useful to end-users.

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USGS2019

Seasonal, spring-neap, and tidal variation in cohesive sediment transport parameters in estuarine shallows

Numerical models for predicting sediment concentrations and transport rely on parameters such as settling velocity and bed erodibility that describe sediment characteristics, yet these parameters are rarely probed directly. We investigated temporal and spatial variation in sediment parameters in the shallows of San Pablo Bay, CA. Flow, turbulence, and suspended sediment data were measured at sites located at 1 and 2 m below mean lower low water (MLLW) from November 2013 through April 2015, supplemented by monthlong periods in 2011, 2012, and 2016. Maximum current velocities were 0.40–0.47 m s -1 at these depths; the strongest currents decreased to 0.27–0.34 m s -1 during neap periods. Winters 2013–2014 and 2014–2015 experienced strong drought conditions, limiting the potential for seasonal impact on sediment conditions during this experiment. Despite this, the more storm‐influenced site showed clear changes during the winter: the roughness parameter decreased from 10 −4 to 10 −5 m, from hydrodynamically rough to smooth conditions, and bed erodibility increased by an order of magnitude. Median settling velocity was 2.05·10 −4 m s -1 ; it varied twofold within a tidal cycle, decreasing as current velocity grew during flood and ebb. This tidal control on floc size affected settling velocity on the spring‐neap timescale, possibly driving a spring‐neap oscillation in erodibility. Our findings highlight variation in sediment dynamics that is commonly ignored in numerical models and the need for field observations to ground truth ongoing modeling efforts.

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USGS2019

Measuring settling velocity in a strongly tidal estuary

Predicting sediment transport in estuarine systems requires understanding sediment settling velocity, its range of fluctuations, and the shortcomings of the tools to measure it. Previous studies have used Laser In-Situ Scattering and Transmissometry (LISST) instruments to measure particle size and Acoustic Doppler Velocimeters (ADV) to return estimates of settling velocity. We deployed both instruments over a 4-week period in summer 2016 in San Pablo Bay, CA, and observed conflicting results from the two instruments. The LISST indicated the settling velocity decreased with increasing bed shear stress, while the ADV showed that settling velocity increased. Comparing the experimental conditions from this study with previous research reveals that the ADV method requires steady state conditions that were not achieved. Although the ADV method uses easily measured quantities to return the settling velocity, it relies on assumptions that are not always valid in estuarine settings.

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USGS2016

Marine magnetic survey and onshore gravity and magnetic survey, San Pablo Bay, northern California

Introduction From November 2011 to August 2015, the U.S. Geological Survey (USGS) collected more than 1,000 line-kilometers (length of lines surveyed in kilometers) of marine magnetic data on San Pablo Bay, 98 onshore gravity stations, and over 27 line-kilometers of ground magnetic data in northern California. Combined magnetic and gravity investigations were undertaken to study subsurface geologic structures as an aid in understanding the geologic framework and earthquake hazard potential in the San Francisco Bay Area. Furthermore, marine magnetic data illuminate local subsurface geologic features in the shallow crust beneath San Pablo Bay where geologic exposure is absent. Magnetic and gravity methods, which reflect contrasting physical properties of the subsurface, are ideal for studying San Pablo Bay. Exposed rock units surrounding San Pablo Bay consist mainly of Jurassic Coast Range ophiolite, Great Valley sequence, Franciscan Complex rocks, Miocene sedimentary rocks, and unconsolidated alluvium (Graymer and others, 2006). The contrasting magnetic and density properties of these rocks enable us to map their subsurface extent.

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USGS2014

Interactions between waves, sediment, and turbulence on a shallow estuarine mudflat

Measurements were collected on a shallow estuarine mudflat in northern San Francisco Bay to examine the physical processes controlling waves, turbulence, sediment resuspension, and their interactions. Tides alone forced weak to moderate currents of 10–30 cm s -1 in depths of 0–3 m, and maintained a background suspension of 30–50 mg L21 of fine sediment. In the presence of wind waves, bottom orbital velocities spanned 20–30 cm s -1 , suspended-sediment concentrations (SSC) at 15 and 30 cm above the bed (cmab) increased by 1–2 orders of magnitude, and vertical gradients in SSC were strong enough to produce turbulence-limiting stratification, with gradient Richardson numbers exceeding 0.25. Simultaneously, turbulent stresses (decomposed from wave motions) increased by an order of magnitude. The apparent contradiction of energetic turbulence in the presence of strong stratification was reconciled by considering the turbulent kinetic energy (TKE) budget: in general, dissipation and buoyancy flux were balanced by local shear production, and each of these terms increased during wave events. The classic wave-current boundary layer model represented the observations qualitatively, but not quantitatively since the velocity profile could not be approximated as logarithmic. Rather, the mean shear was elevated by the Stokes drift return flow and wind-generated surface stress, which diffused sediment upward and limited stratification. Our findings highlight a pathway for waves to supply energy to both the production and destruction of turbulence, and demonstrate that in such shallow depths, TKE and SSC can be elevated over more of the water column than predicted by traditional models.

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USGS2010

Bed composition generation for morphodynamic modeling: Case study of San Pablo Bay in California, USA

Applications of process-based morphodynamic models are often constrained by limited availability of data on bed composition, which may have a considerable impact on the modeled morphodynamic development. One may even distinguish a period of “morphodynamic spin-up” in which the model generates the bed level according to some ill-defined initial bed composition rather than describing the realistic behavior of the system. The present paper proposes a methodology to generate bed composition of multiple sand and/or mud fractions that can act as the initial condition for the process-based numerical model Delft3D. The bed composition generation (BCG) run does not include bed level changes, but does permit the redistribution of multiple sediment fractions over the modeled domain. The model applies the concept of an active layer that may differ in sediment composition above an underlayer with fixed composition. In the case of a BCG run, the bed level is kept constant, whereas the bed composition can change. The approach is applied to San Pablo Bay in California, USA. Model results show that the BCG run reallocates sand and mud fractions over the model domain. Initially, a major sediment reallocation takes place, but development rates decrease in the longer term. Runs that take the outcome of a BCG run as a starting point lead to more gradual morphodynamic development. Sensitivity analysis shows the impact of variations in the morphological factor, the active layer thickness, and wind waves. An important but difficult to characterize criterion for a successful application of a BCG run is that it should not lead to a bed composition that fixes the bed so that it dominates the “natural” morphodynamic development of the system. Future research will focus on a decadal morphodynamic hindcast and comparison with measured bathymetries in San Pablo Bay so that the proposed methodology can be tested and optimized.

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USGS2010

Measuring sediment accretion in early tidal marsh restoration

Sediment accretion is a critical indicator of initial progress in tidal marsh restoration. However, it is often difficult to measure early deposition rates, because the bottom surface is usually obscured under turbid, tidally-influenced waters. To accurately measure early sediment deposition in marshes, we developed an echosounder system consisting of a specialized acoustic profiler, differential global positioning system unit, and laptop computer mounted on a shallow-draft boat. We conducted a bathymetry at the Tubbs Setback tidal restoration site on San Pablo Bay, California, along north–south transects at 25-m intervals. Horizontal position was recorded within 1 m each second and water depth to 1 cm every 0.05 s. Bottom elevations were adjusted for tidal height with surveyed tide gages. We created detailed bathymetric maps (grid cell size: 12.5 m x 12.5 m) by interpolation with inverse distance weighting. During the third year after restoration, sediment accretion averaged 57.1 ± 1.1 cm and the estimated sediment gain was 132,900 m3. The mean difference between the elevations from the bathymetry system and the 9 sediment pins was 2.0 ± 1.0 cm. The mean difference of the intersection points of east–west and north–south survey transects was 2.1 ± 0.2 cm, which provided a measure of repeatability with changing water levels. Our echosounder system provided accurate and repeatable measurements of sediment accretion of a recently restored tidal wetland, and this system proved to be a viable tool for determining sediment deposition in marshes and assessing early restoration progress.

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USGS2003

Microbial cycling of mercury in contaminated pelagic and wetland sediments of San Pablo Bay, California

San Pablo Bay is an estuary, within northern San Francisco Bay, containing elevated sediment mercury (Hg) levels because of historic loading of hydraulic mining debris during the California gold-rush of the late 1800s. A preliminary investigation of benthic microbial Hg cycling was conducted in surface sediment (0–4 cm) collected from one salt-marsh and three open-water sites. A deeper profile (0–26 cm) was evaluated at one of the open-water locations. Radiolabeled model Hg-compounds were used to measure rates of both methylmercury (MeHg) production and degradation by bacteria. While all sites and depths had similar total-Hg concentrations (0.3–0.6 ppm), and geochemical signatures of mining debris (as εNd, range: –3.08 to –4.37), in-situ MeHg was highest in the marsh (5.4±3.5 ppb) and ≤0.7 ppb in all open-water sites. Microbial MeHg production (potential rate) in 0–4 surface sediments was also highest in the marsh (3.1 ng g –1 wet sediment day –1 ) and below detection (<0.06 ng g –1 wet sediment day –1 ) in open-water locations. The marsh exhibited a methylation/demethylation (M/D) ratio more than 25× that of all open-water locations. Only below the surface 0–4-cm horizon was significant MeHg production potential evident in the open-water sediment profile (0.2–1.1 ng g –1 wet sediment day –1 ). In-situ Hg methylation rates, calculated from radiotracer rate constants, and in-situ inorganic Hg(II) concentrations compared well with potential rates. However, similarly calculated in-situ rates of MeHg degradation were much lower than potential rates. These preliminary data indicate that wetlands surrounding San Pablo Bay represent important zones of MeHg production, more so than similarly Hg-contaminated adjacent open-water areas. This has significant implications for this and other Hg-impacted systems, where wetland expansion is currently planned.

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USGS2002

Comparison of the basin-scale effect of dredging operations and natural estuarine processes on suspended sediment concentration

Suspended sediment concentration (SSC) data from San Pablo Bay, California, were analyzed to compare the basin-scale effect of dredging and disposal of dredged material (dredging operations) and natural estuarine processes. The analysis used twelve 3-wk to 5-wk periods of mid-depth and near-bottom SSC data collected at Point San Pablo every 15 min from 1993-1998. Point San Pablo is within a tidal excursion of a dredged-material disposal site. The SSC data were compared to dredging volume, Julian day, and hydrodynamic and meteorological variables that could affect SSC. Kendall's ??, Spearman's ??, and weighted (by the fraction of valid data in each period) Spearman's ??w correlation coefficients of the variables indicated which variables were significantly correlated with SSC. Wind-wave resuspension had the greatest effect on SSC. Median water-surface elevation was the primary factor affecting mid-depth SSC. Greater depths inhibit wind-wave resuspension of bottom sediment and indicate greater influence of less turbid water from down estuary. Seasonal variability in the supply of erodible sediment is the primary factor affecting near-bottom SSC. Natural physical processes in San Pablo Bay are more areally extensive, of equal or longer duration, and as frequent as dredging operations (when occurring), and they affect SSC at the tidal time scale. Natural processes control SSC at Point San Pablo even when dredging operations are occurring.

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USGS1998

Sedimentation and bathymetric change in San Pablo Bay: 1856-1983

A long-term perspective of erosion and deposition in San Francisco Bay is vital to understanding and managing wetland change, harbor and channel siltation, and other sediment-related phenomena such as particle and particle-associated substance (pollutants, trace metals, etc.) transport and deposition. A quantitative comparison of historical hydrographic surveys provides this perspective. This report presents results of such a comparison for San Pablo Bay, California. Six hydrographic surveys from 1856 to 1983 were analyzed to determine long-term changes in the sediment system of San Pablo Bay. Each survey was gridded using surface modeling software. Changes between survey periods were computed by differencing grids. Patterns and volumes of erosion and deposition in the Bay are derived from difference grids. More than 350 million cubic meters of sediment was deposited in San Pablo Bay from 1856 to 1983. This is equivalent to a Baywide accumulation rate of approximately 1 cm/yr. However, sediment deposition was not constant over time or throughout the Bay. Over two-thirds of that sediment was debris from hydraulic mining that accumulated from 1856 to 1887. During this period, deposition occurred in nearly the entire Bay. In contrast, from 1951 to 1983 much of the Bay changed from being depositional to erosional as sediment supply diminished and currents and waves continued to remove sediment from the Bay. The decrease in sediment supply is likely the result of upstream flood-control and water-distribution projects that have reduced peak flows, which are responsible for the greatest sediment transport. One consequence of the change in sedimentation was a loss of about half of the tidal flat areas from the late 1800's to the 1980's. Change in sedimentation must also have affected flow in the Bay, areas where polluted sediments were deposited, exchange of sediment between the nearshore and wetlands, and wave energy reaching the shoreline that was available to erode wetlands. Further work is needed. Studies of historical wetland change and the relationship between change and man-made and natural influences would be valuable for developing sound wetland management plans. Additionally, extending the historical hydrographic and wetland change analyses eastward into Suisun Bay will improve the understanding of the North Bay sediment system.

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