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Marsh Vegetation Surveys Across the San Francisco Bay Estuary, 2008-2018

April 16, 2024

Fifty-one tidal marsh sites across five regions (sub-embayments) were surveyed in the Delta, Suisun Bay, San Pablo Bay, central San Francisco Bay, and South San Francisco Bay. Vegetation surveys spanned ten years, from July 2008 to January 2018. A total of 5,112 plots were surveyed. Plots were positioned on transects along an elevation gradient and evenly distributed across each site, where possible, to capture spatial variability along elevation and distance gradients. At each plot, percent cover of all plant species, bare ground, and litter as well as average height was visually assessed within a 0.25 m2 quadrat. Total plant cover in a plot could exceed 100 percent due to vegetation layering. Bare ground and litter cover was estimated as total area visible through the vegetation from above the plot. Vascular plant nomenclature followed Baldwin et al. (2012). Average plant height (in meters) was recorded at most sites. Geographic position (in UTM) and elevation (North American Vertical Datum of 1988, NAVD88) were recorded at each plot. Channel salinity was calculated at the site or multi-site scale (in PSU) with data from locally deployed water sensors or from San Francisco Bay National Estuarine Research Reserve (NERR) sites (Takekawa et al. 2013, Thorne et al. 2019). All salinity values represent marsh channel or creek conditions, and not soil porewater salinity. A survey-grade Real Time Kinematic (RTK) global positioning systems (GPS) rover was used to measure location and elevation (plus or minus 1 cm horizontal, plus or minus 2 cm vertical manufacturer-stated accuracy; Leica Geosystems Inc., Norcross, Georgia). Rover positions were received in real time from the Leica Smartnet system using a CDMA modem ( The WGS 84 ellipsoid model was used for horizontal positioning and NAVD88 for vertical positioning. Rover accuracy and precision were evaluated by measuring positions at local National Geodetic Survey benchmarks; all errors were within the stated rover error. Elevation data was converted to z*, a unitless measure of elevation relative to the local tidal frame which accounts for variation in tidal range and allows for direct comparison across sites (Swanson et al. 2014). Local tidal datums were calculated from multiple sources including NOAA tide stations (, deployed water level loggers, and NOAA’s VDATUM model (Parker et al. 2003). Distance to channel was calculated as the distance (in meters) between each plot and the digitalized boundaries of all nearby channels and bays. Channels were digitized based on 2020 NAIP imagery supplemented with LiDAR when necessary. The centerline was digitized on small channels (appox. 1 - 2.5 m wide), while both edges were digitized on large channels (greater than 2.5 m), bays, and rivers.

Baldwin B. G., Goldman D. H., Keil D. J., Patterson R., Rosatti T. J. (2012). The Jepson manual: vascular plants of California. (Berkeley: University of California Press).

Parker B., Milbert D., Hess K., Gill S. (2003). National VDatum–The implementation of a national vertical datum transformation database. Silver Spring: National Oceanic and Atmospheric Administration, National Ocean Service. 9.

Swanson K. M., Drexler J. Z., Schoellhamer D. H., Thorne K. M., Casazza M. L., Overton C. T., et al. (2014). Wetland accretion rate model of ecosystem resilience (WARMER) and its application to habitat sustainability for endangered species in the San Francisco estuary. Estuaries Coasts 37, 476–492. doi: 10.1007/s12237-013-9694-0

Takekawa J. Y., Thorne K. M., Buffington K. J., Freeman C. M., Powelson K. W., Block G. (2013). Assessing marsh response from sea-level rise applying local site conditions: Humboldt Bay National Wildlife Refuge. Unpubl. Data Summary Report (Vallejo, CA: USGS Western Ecological Research Center). 44pp + Appendices.

Thorne K. M., Backe K. E., Freeman C. M., Buffington K. J., Forstner T. M., Goodman A. C. (2019). Don Edwards National Wildlife Refuge Vegetation, Elevation, Inundation Inventory to Inform Sea-level Rise Vulnerability. Unpubl. Data Summary Report (Davis, CA: USGS Western Ecological Research Center). 112pp.

These data support the following publication:
Rankin, L.L., Jones, S.F., Janousek, C.N., Buffington, K.J, Takekawa, J.Y., and Thorne, K.M., 2023. Stress gradients structure spatial variability in coastal tidal marsh plant composition and diversity in a major Pacific coast estuary. Frontiers in Ecology and Evolution, 11.

Publication Year 2024
Title Marsh Vegetation Surveys Across the San Francisco Bay Estuary, 2008-2018
DOI 10.5066/P94F802H
Authors Lyndsay L Rankin, Scott F Jones, Christopher N Janousek, Kevin J Buffington, John Y Takekawa, Karen M Thorne
Product Type Data Release
Record Source USGS Digital Object Identifier Catalog
USGS Organization Western Ecological Research Center - Headquarters