A three-dimensional hydrodynamic and sediment transport model of San Pablo and Suisun Bays was constructed using the Delft3D4 (D3D) modeling suite (Deltares, 2021a) to simulate water levels, flow, waves, and suspended sediment for time period of Nov 1 to Dec 31, 2014. This data release describes the construction and validation of the model application and provides input files suitable to run the model on D3D software version 4.04.01.

A one- and two-dimensional hydrodynamic model of the San Francisco Bay and Delta was constructed using the Delft3D Flexible Mesh Suite (Delft3D FM; Kernkamp and others, 2011; https://www.deltares.nl/en/software/delft3d-flexible-mesh-suite/) to simulate still water levels. Required model input files are provided to run the model for the time period from October 1, 2018, to April 30, 2019. This data release describes the construction and validation of the model application and provides input files suitable to run the model on Delft3D FM Suite 2020.04. Model Description: The San Francisco Bay and Delta Still Water Level Model (SFBD-SWL) utilizes the open-source Delft3D Flexible Mesh Suite (Delft3D FM; Kernkamp and others, 2011; https://www.deltares.nl/en/software/delft3d-flexible-mesh-suite/, 2020.04 release, SVN revision 601351) to compute Still Water Levels (SWLs) in San Francisco Bay and the Sacramento-San Joaquin Delta. SWL captures the effects of meteorological and fluvial forcing on the coastal water levels; however, it excludes the impacts of wave setup and runup on the water level. The model covers the Delta up to the approximate upstream limit of tidal influence and extends seaward to the Pacific Ocean. It must be noted that the main purpose of the model was to simulate SWL in open embayments of the San Francisco Bay. The model utilizes 1D elements used to represent tributaries and rivers flowing into the Bay and Delta. Model schematizations of the Delta (model grid and cross-section profiles) were derived from Delta Simulation Model II (DSM2, California Department of Water Resources, 2013). Topographic and bathymetric datasets from the USGS and California Department of Water Resources were applied across the San Francisco Bay and Delta Hydrodynamic model. In particular, the 2-meter resolution LEAN-corrected topography in the Bay (Buffington and others, 2016) and the seamless 10-meter resolution digital elevation model by Fregoso and others (2017) were applied. Data from the National Land Cover Database Land Cover (CONUS; Homer and others, 2020) were converted to roughness. The unstructured grid consists of more than 185,000 net nodes in the horizontal with a spatial resolution as fine as 100 meters. The 100-meter resolution model network is not fine enough to resolve smaller features such as narrow levees and dams. Therefore, an additional polyline has been included to account for constraining and rerouting effects of local levees and infrastructure. This file provides the location of each subgrid feature and, in combination with the latest topography, describes fine-scale elevations for the hydrodynamic simulations. The model is forced by astronomic tides and remote non-tidal residual (NTR) water levels at the offshore boundaries, fluvial discharges, and wind and atmospheric mean sea level pressure fields at the surface. Offshore Boundaries The model's offshore boundary conditions in the Pacific Ocean are based on 67 measured tidal constituents at San Francisco with spatial variability derived from TPXO 8.0 (Egbert and Erofeeva, 2002). Tidal constituents were calibrated based on the difference between modeled and observed tidal constituents at the NOAA tide stations located throughout the bay. Remote NTR derived from measurements at the San Francisco NOAA tide station (#9414290) are applied uniformly across the ocean boundary. The tidal forcing files are included in the model package, as well as the NTR offshore boundary forcing files for the time period from Oct-2018 to Apr-2019. Discharge Boundaries Fluvial discharges from 16 USGS gauged rivers that flow into the Bay are included in the model (https://waterdata.usgs.gov/nwis/dv/?referred_module=sw). Six fluvial inflows to the Delta are based on Dayflow model outputs (https://data.ca.gov/dataset/dayflow). The discharge forcing files for the time period from Oct-2018 to Apr-2019 are included in the model package. The discharge stations incorporated in the SFBD-SWL are

The U.S. Geological Survey Pacific Coastal and Marine Science Center collected data to investigate sediment dynamics in the shallows of San Pablo Bay in two deployments: February to March 2011 (ITX11) and May to June 2012 (ITX12). This data release includes time-series data and grain-size distributions from sediment grabs collected during the deployments. During each deployment, time series of current velocity, water depth, and turbidity were collected at several stations in the shallows, and one station in the channel. Velocity and depth (pressure) were collected at high frequency (10 Hz) to allow calculation of wave parameters and turbulence statistics.

The U.S. Geological Survey Pacific Coastal and Marine Science Center collected data to investigate sediment dynamics in the shallows of San Pablo Bay in two deployments: February to March 2011 (ITX11) and May to June 2012 (ITX12). This data release includes time-series data and grain-size distributions from sediment grabs collected during the deployments. During each deployment, time series of current velocity, water depth, and turbidity were collected at several stations in the shallows, and one station in the channel. Velocity and depth (pressure) were collected at high frequency (10 Hz) to allow calculation of wave parameters and turbulence statistics.

This portion of the USGS data release contains simulated nearshore wave parameters derived from a stand-alone spectral wave model of the Columbia River littoral cell, Washington and Oregon. The model output includes significant wave heights, peak wave periods, mean wave directions, and water depths for a series of 221 shore normal transects that extended from the coastline to the -15 m NAVD88 elevation (about 16.5 m average water depth). Data are provided at the seaward extent of each transect as well as at the location of the break point, or location just outside the surf zone, which varied dynamically based on the local bathymetry and wave conditions. Additional data are provided at four locations corresponding to the locations of buoy observations used to validate the model application. The data are derived from two hindcasts solved at hourly intervals between 1) August 2014 to September 2023 (h1), and 2) July 2010 to August 2011 (h2). The data from both hindcasts were compiled into netCDF files for the nearshore and buoy locations for distribution.

This portion of the USGS data release contains simulated nearshore wave parameters derived from a stand-alone spectral wave model of the Columbia River littoral cell, Washington and Oregon. The model output includes significant wave heights, peak wave periods, mean wave directions, and water depths for a series of 221 shore normal transects that extended from the coastline to the -15 m NAVD88 elevation (about 16.5 m average water depth). Data are provided at the seaward extent of each transect as well as at the location of the break point, or location just outside the surf zone, which varied dynamically based on the local bathymetry and wave conditions. Additional data are provided at four locations corresponding to the locations of buoy observations used to validate the model application. The data are derived from two hindcasts solved at hourly intervals between 1) August 2014 to September 2023 (h1), and 2) July 2010 to August 2011 (h2). The data from both hindcasts were compiled into netCDF files for the nearshore and buoy locations for distribution.

A three-dimensional hydrodynamic and sediment transport model application of the mouth of the Columbia River (MCR) was constructed using the Delft3D4 (D3D) modeling suite (Deltares, 2021) to simulate water levels, flow, waves, and sediment transport for time period of September 22, 2020, to March 10, 2021. The model was used to predict the dispersal of sediment from a submerged, nearshore berm composed of sediment that was dredged from the entrance to the MCR navigation channel and placed on the northern flank of the ebb-tidal delta. This data release describes the development and validation of the model application and provides input files suitable to run the models on D3D software version 4.04.01. These data accompany Stevens and others (2023).

A three-dimensional hydrodynamic and sediment transport model application of the mouth of the Columbia River (MCR) was constructed using the Delft3D4 (D3D) modeling suite (Deltares, 2021) to simulate water levels, flow, waves, and sediment transport for time period of September 22, 2020, to March 10, 2021. The model was used to predict the dispersal of sediment from a submerged, nearshore berm composed of sediment that was dredged from the entrance to the MCR navigation channel and placed on the northern flank of the ebb-tidal delta. This data release describes the development and validation of the model application and provides input files suitable to run the models on D3D software version 4.04.01. These data accompany Stevens and others (2023).

A coupled coastal hydrodynamic and sediment transport model application was constructed using the Delft3D (version 4.04.01) modeling system to simulate dispersal of fine-grained sediment plumes from beach nourishment projects along the coast of Santa Barbara, California. The model consisted of a three-dimensional Delft3D flow model that was 2-way coupled to the spectral wave model, SWAN, computed on a structured curvilinear grid with a spatial resolution that varied between 20 m in the nearshore area near the project site to about 180 m at the seaward extent of the model domain. Dispersal of fine-grained sediment plumes was simulated for two types of nourishment projects including drag and haul (DH) and hydraulic dredging (HD) that are periodically performed to increase the supply of sediment to beaches in the study area. The modeling approach utilized two types of simulations including a series of relatively short (3-day) sensitivity tests to examine variability in plume direction and extent under variations in wind direction, wave height, and sediment settling velocities as well as longer (3 month) hindcasts to simulate sediment dynamics associated with typical nourishment projects using realistic wave and wind conditions. Model input files for both drag and haul (DH) and hydraulic dredging (HD) projects are provided in .zip archives for both sensitivity and hindcast simulations.

Sediment cores were collected from San Pablo Bay, in the Sacramento-San Joaquin Delta in California by the U.S. Geological Survey Pacific Coastal and Marine Science Center (PCMSC) during multiple surveys from 2011 to 2012. The cores were analyzed for grain-size distributions at the PCMSC sediment lab.