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San Francisco Bay Benthic Macroinvertebrate Atlas


San Francisco Bay Benthic Macroinvertebrate Atlas

By Aariel Rowan1, K. Benjamin Gustafson2, William M. Perry2, Susan W. De la Cruz2, Janet K. Thompson3, John Y. Takekawa2

U.S. Department of the Interior
Ken Salazar, Secretary

U.S. Geological Survey
Marcia McNutt, Director 

Western Ecological Research Center
Steven Schwarzbach, Director

1 San Francisco State University, Department of Geography and Environmental Science, 1600 Holloway Avenue, San Francisco, CA 94132

2 U.S. Geological Survey, Western Ecological Research Center , Dixon Field Station, 6924 Tremont Road, Dixon, CA 95620; and San Francisco Bay Estuary Field Station, 505 Azuar Drive, Vallejo, CA 94592

3 U.S Geological Survey, Water Resources, National Research Program, 345 Middlefield Road, Menlo Park, CA 94025

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Suggested citation: Rowan, A., K.B. Gustafson, W.M. Perry, S.W. De la Cruz, J.K. Thompson, and J.Y. Takekawa. 2011. Spatial database for the distribution and abundance of benthic macroinvertebrates in the San Francisco Bay. San Francisco State University, San Francisco, CA; U.S. Geological Survey, Western Ecological Research Center, Dixon and Vallejo; and U.S. Geological Survey, National Research Program, Menlo Park, CA.



The San Francisco Bay is the largest estuary on the Pacific coast of North America and is vitally important for wintering and migrating water birds, particularly diving ducks. As much as 50% of several diving duck populations in the lower Pacific Flyway winter in the estuary, and they are key predators on subtidal and intertidal macroinvertebrates. Many North American diving duck species are in decline, and changing winter and spring habitat conditions have been implicated as a potential contributing factor. The SFB estuary has undergone extensive degradation resulting from human growth and development, and these alterations are all threats to intertidal and subtidal habitats used by diving duck populations.

From 2007-2010, San Francisco State University and the U.S. Geological Survey gathered benthic macroinvertebrate distribution data from a number of different organizations in an attempt to document prey availability for SFB benthic predators (including the greater and lesser scaup (Aythya marila, Aythya affinis), surf scoter (Melanitta perspicillata), and canvasback (Aythya valisineria).   Local, state, and federal research agencies and non- profits contributed data for this analysis. Along with existing macroinvertebrate prey distribution data, we have also included information on the physical characteristics of the benthic environment (salinity, elevation, sediment composition).

While compiling datasets used to calculate the carrying capacity of diving ducks in the SFB, we realized that this collection could serve as a helpful resource for other researchers and resource managers.  This system was modeled on an earlier summary of seabird and marine mammal off Southern California (Takekawa et al. 2004, Mason et al. 2007) presented in 2009 ( and a summary of Pacific fisheries datasets released in 2010 (

Benthic Macroinvertebrate Datasets

We included macroinvertebrate (organisms greater than 0.5mm) abundance, biomass and distribution information collected from the benthic zone of the San Francisco Bay.  All macroinvertebrate data have been stored as tables inside a geodatabase and tied to spatial locations via relationship classes.  Benthic Macroinvertebrate data were contributed by the following organizations:

  • USGS National Research Program (1988-2009)
  • USGS WERC San Francisco Bay Estuary Field Station (2003-2005)
  • California Department of Water Resources (1990, 1993, 1995)
  • University of  Wyoming (1999-2000)
  • San Francisco Estuary Institute (1975-2006) compilation includes data from the
    • National Oceanic and Atmospheric Administration (2000-2001)
    • California Department of Water Resources (1975-2006)
    • Bay Area Dischargers Association (1994-1997)
    • Bay Protection and Toxic Cleanup Program (1992, 1997)
    • SFEI Regional Monitoring Program (1994-2003)
    • SFEI Coastal Intensive Sites Network (2000-2001)
  • California Academy of Science Institute of Zoology data (1903-2005)

Additional Datasets

  • USGS San Francisco Bay Bathymetry
  • USGS Sediment type and grain size (2004-2005, 2008)
  • USGS Water Quality (1997-2002)
  • Fish collections from the California Academy of Science (1889-2007)
  • Fish collections from Marine Science Institute (2003-2008)



This project was supported by the San Francisco Foundation and Oikonos Ecosystem Knowledge.  Macroinvertebrate data for this project was generously provided by the US Geologic Survey, Western Ecological Research Center, San Francisco Bay Estuary Field Station (Susan W. De la Cruz, John Takekawa); USGS National Research Program, Menlo Park (Janet K. Thompson and Francis Parchaso); San Francisco Estuary Institute, Regional Monitoring Program (program manager Meg Sedlak, lead scientist Jay Smith, and Sarah Lowe compiled data from the National Oceanic and Atmospheric Administration, U.S. Environmental Protection Agency, California Department of Water Resources, Bay Area Dischargers Association, Bay Protection and Toxic Cleanup Program, and several SFEI programs); Department of Water Resources, Corbula Blitz (Karen Gehrts); University of Wyoming, Department of Zoology (Victoria Poulton, Jim Lovvorn, and John Y. Takekawa); California Academy of Sciences Institute of Zoology (Robert Van Syoc).  Data on Fish abundance and distribution was provided by the California Academy of Sciences, Department of Ichthyology (Jon D. Fong); and the Marine Sciences Institute (Aaron Tinker).  Physical datasets were generously provided by the U.S. Geological Survey, Pacific Coastal and Marin Science Center (Bathymetry by Bruce Jaffe and Rich Smith, Grain Size and Sediment type by Patrick Barnard, and Jane Reid with usSeabed) and Water Resources (Tara Schraga).


For additional information, contact:
William M. Perry
U.S. Geological Survey, Western Ecological Research Center
Dixon Field Station
6924 Tremont Rd
Dixon, CA 95620
Telephone: (707) 678-0682 ext 619
Fax: (707) 678-5039


John Y. Takekawa
USGS Western Ecological Research Center
San Francisco Bay Estuary Field Station
505 Azuar Drive
Vallejo, CA 94592
Tel: (707) 562-2000; Fax: (707) 562-3001


Information in this Benthic Atlas may be cited and analyzed for summary reports but not used for scientific publication without permission from the original authors. Please cite the original contributors and authors in the metadata if these data are used or included in developed products excluding scientific papers.

The macroinvertebrate, fish, and physical data contained on this website may only be used within the context of the included ArcMap document. For specific use constraints of each dataset, please see the metadata. The original data providers must be contacted for future updates.

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