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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 (USGS) in partnership with the New Jersey Department of Environmental Protection.

Ilustrated map of a shoreline with symbols drawn on it to show various data points.
Coast of New Jersey, showing Barnegat Bay-Little Egg Harbor estuary and its three inlets—(from north to south) Manasquan, Barnegat, and Little Egg—and locations of USGS hydrologic monitoring stations. Color-coded depths in estuary are gridded data from the National Oceanic and Atmospheric Administration (NOAA) Estuarine Data Set. Acquired in the 1930s, these are the latest comprehensive bathymetric data collected in the estuary before the current survey.

by Jennifer Miselis, Brian Andrews, Neil Ganju, Anthony Navoy, Robert Nicholson, and Zafer Defne

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 (USGS) in partnership with the New Jersey Department of Environmental Protection. The agencies began this collaboration in response to New Jersey Governor Chris Christie's plan to clean up Barnegat Bay, set into motion in December 2010 (State of New Jersey DEP; Barnegat Bay). The ongoing study will also yield insights into the impacts of Hurricane Sandy, which made landfall southwest of the study area on October 29, 2012. (Read "Hurricane Sandy Disrupts USGS Study of the Barnegat Bay-Little Egg Harbor Estuary in New Jersey, Provides Additional Research Opportunities.")

The narrow estuary—71 kilometers (44 miles) long and a maximum of 6 kilometers (4 miles) wide—is bounded on the west by the mainland and on the east by barrier islands that constitute much of the Jersey Shore. The estuary covers approximately 340 square kilometers (130 square miles), with a mean depth of less than 1 meter (3 feet). This long body of water, 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 tides. Added to these problems is uncertainty about how the planned removal of the Oyster Creek nuclear power plant, which discharges heated water into the estuary, will alter the estuary's thermal structure. 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 sediment on and beneath the seafloor) and modeling how the physical characteristics interact to affect the estuary's water quality.

Scientists from the 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 continued the mapping in March 2012. With funding from the New Jersey Department of Environmental Protection and logistical support from the USGS New Jersey Water Science Center, they collected data with a suite of geophysical tools, such as a 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. (For additional information, visit the Woods Hole Sea Floor Mapping Group web site.)

The resulting data provide the first comprehensive look at the estuary's morphology (shape of shore and seafloor) and geology (composition and geometry of seafloor and subseafloor materials). The mapping effort, to be completed in March 2013, is using marine and airborne sensors to collect high-resolution depth and elevation data, as well as data on seafloor and subseafloor composition. Together, these data will help reveal the geologic history of the estuary and provide a context for understanding modern processes that affect its water circulation. To date, the scientists have mapped approximately 85 square kilometers (33 square miles) of the estuary and have collected numerous samples and detailed photographs of the seafloor. Publication of the complete seafloor-mapping dataset is expected in late 2013. The data have already shown connections between the subseafloor geology and the modern distribution of sediments within the estuary, which may profoundly affect recruitment of shellfish, distribution of seagrasses, and persistence of pollutants.


Two people preparing a sonar device on a small boat at the dock.
USGS scientists Bill Danforth (standing, left) and Chuck Worley (crouching on deck) deploy a swath bathymetric sonar from the bow of the research vessel (R/V) Raphael, a boat from the USGS Woods Hole Coastal and Marine Science Center used for seafloor mapping and sediment sampling, docked at Dillon's Creek Marina in Island Heights, New Jersey. Danforth led a tour of the vessel and its scientific equipment for local news reporters and visitors from the New Jersey Department of Environmental Protection and the USGS New Jersey Water Science Center during the first survey in November 2011.
Shoreline map and photos to show various data.
Shoreline of Barnegat Bay, showing color-coded USGS bathymetric data (deeper toward blue end of spectrum, shallower toward red end) collected in November 2011 and March 2012, and locations of bottom-sediment-sampling stations (black dots) visited in March 2012. Despite a survey-trackline spacing of 50 meters (55 yards), 100-percent bathymetric coverage of the estuary seafloor was impossible because of the estuary's shallow depths. Inset A, Detailed bathymetry of channel leading out to Barnegat Inlet, with numerous bedforms, such as sand waves, lining channel floor. Inset B, Subset of the sidescan-sonar data, which achieved 100-percent coverage of the estuary seafloor. Analysis of sediment samples shows that lower backscatter (darker in this image) represents silt and higher backscatter (lighter) represents silty sand. Yellow dashed lines delineate zone of low backscatter that overlies relict tidal channels mapped beneath the estuary's seafloor, indicating a link between the geologic history of the estuary and modern sediment distribution.
Map of the seafloor showing patterns in the sediment.
Barnegat Inlet, showing changes in the inlet navigation channel and island morphology between the 1930s (yellow) and 2011 (red). A north-south dike, shown here as a green ridge between the red and yellow lines (also shown in inset A of previous figure), was added in the 1930s to create a straighter path for the channel.

Personnel from the USGS New Jersey Water Science Center are continuously measuring flow, stage (water level), and water quality at strategic sites with funding from the New Jersey Department of Environmental Protection and the USGS Cooperative Water Program (see map at top of page). Flow at the estuary's three ocean inlets and at three bridge crossings is measured by using acoustic Doppler velocity meters (ADVMs). Tidal stage is continuously monitored at seven sites within the bay. These measurements provide detailed information on movement of brackish water through the estuary. Streamflow-gaging stations at seven sites on the major tributary streams provide a continuous record of freshwater flow into the bay. Sixty-eight percent of the area contributing freshwater inflow and 100 percent of the tidal flux between the bay and the Atlantic Ocean are continuously monitored. USGS monitoring stations measure changes in various water-quality parameters, including nitrate concentrations in the largest tributary stream and concentrations of chlorophyll a (an indicator that relates to five algal species groupings: green algae, cyanobacteria, cryptophytes, diatoms, and dinoflagellates) at the northernmost bridge crossing the bay. Additionally, the New Jersey Department of Environmental Protection and other research partners are undertaking a multiyear, weekly water-quality-sampling program in the estuary and its freshwater tributaries.

A platform on four telephone pole piers in calm waters with a USGS placard on top.
USGS tidal-flow-monitoring station at Little Egg Inlet near Beach Haven Heights, New Jersey.

Seafloor-mapping data and hydrologic measurements provide the foundation to develop and calibrate models of the estuary, which predict how the water and sediment within it move in response to tides, storm currents, and other influences. The New Jersey Department of Environmental Protection, the USGS Cooperative Water Program, and the USGS Coastal and Marine Geology Program fund this effort. USGS scientists in Woods Hole are developing a three-dimensional hydrodynamic model of the estuary using the Coupled-Ocean-Atmosphere-Wave-Sediment Transport (COAWST) modeling system to understand circulation and to provide input for a water-quality model being constructed by the USGS New Jersey Water Science Center. The modeling effort is strongly linked with the seafloor-mapping and hydrologic-measurement efforts on several levels. For example, preliminary modeling with historical bathymetry from the early 20th century revealed that tidal dynamics are strongly affected by inlet configuration and bathymetry. Once we updated the inlet configuration with modern aerial photography and bathymetry, the model properly simulated tidal amplitudes within the estuary. The model is updated as new bathymetric data become available, and the sediment-transport-modeling component will rely heavily on data that we collect about bottom sediment, such as its composition and grain size.

The hydrologic measurements being led by the USGS New Jersey Water Science Center provide a critical calibration dataset for the model. New Jersey Water Science Center scientists are using the Water-quality Analysis Simulation Program (WASP) to simulate estuarine water quality. Output from the COAWST hydrodynamic model will prescribe water velocity, tidal levels, temperature, and salinity for the water-quality model through a model linkage being developed as part of the study. Simulated estuarine conditions and processes include dissolved-oxygen concentrations and sediment oxygen consumption (uptake of oxygen by sediment-dwelling organisms), changes in nutrient distribution, changes in sediment nutrient composition, and phytoplankton growth.

The parallel application of mapping, measuring, and modeling ensures that all efforts are complementary and optimized for the widest possible use. Results from this integrated study will help guide efforts to manage and improve water quality in the estuary, as well as provide the framework for many new research projects being conducted by regional, State, and Federal agencies and universities. These projects will shed light on how past, present, and future water quality in the Barnegat Bay-Little Egg Harbor estuary will affect seagrass, benthic invertebrates, phytoplankton, zooplankton, harmful algae, and shellfish. Our initial endeavor, combining expertise in coastal geology, hydrologic science, and physics-based modeling, is a template for fruitful interdisciplinary science by the USGS.

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