Water quality in the Barnegat Bay-Little Egg Harbor estuary along the New Jersey coast is the focus of a multidisciplinary research project begun in 2011 by the U.S. Geological Survey in partnership with the New Jersey Department of Environmental Protection. This narrow estuary is the drainage for the Barnegat Watershed and flushed by just three inlets connecting it to the Atlantic Ocean, is experiencing degraded water quality, algal blooms, loss of seagrass, and increases in oxygen-depletion events, seaweed, stinging nettles, and brown tide. The scale of the estuary and the scope of the problems within it necessitate a multidisciplinary approach that includes characterizing its physical characteristics (for example, depth, magnitude and direction of tidal currents, distribution of seafloor and subseafloor sediment) and modeling how the physical characteristics interact to affect the estuary's water quality. Scientists from USGS Coastal and Marine Geology Program offices in Woods Hole, Massachusetts, and St. Petersburg, Florida, began mapping the seafloor of the Barnegat Bay-Little Egg Harbor estuary in November 2011 and completed in September 2013. With funding from the New Jersey Department of Environmental Protection and logistical support from the USGS New Jersey Water Science Center, data were collected with a suite of geophysical tools, including swath bathymetric sonar for measuring seafloor depth, a sidescan sonar for collecting acoustic-backscatter data (which provides information about seafloor texture and sediment type), and a subbottom profiler for imaging sediment layers beneath the floor of the estuary. More information about the individual USGS surveys conducted as part of this study can be found on Woods Hole Coastal and Marine Science Center Field Activity webpages: >2011-041-FA: http://woodshole.er.usgs.gov/operations/ia/public_ds_info.php?fa=2011-041-FA >2012-003-FA: http://woodshole.er.usgs.gov/operations/ia/public_ds_info.php?fa=2012-003-FA >2013-014-FA: http://woodshole.er.usgs.gov/operations/ia/public_ds_info.php?fa=2013-014-FA >2013-030-FA: http://woodshole.er.usgs.gov/operations/ia/public_ds_info.php?fa=2013-030-FA