Geochemical data were obtained to investigate the fate and transport of nitrogen in a subterranean estuary near East Falmouth, Massachusetts. The goal of this investigation was to assess nitrogen attenuation in the aquifer under the Eel River estuary and the adjacent peninsula. Inorganic nitrogen was introduced to the subterranean estuary from residential septic systems and legacy cesspools.. Groundwater-quality data were collected from three transects from a total of twenty-seven locations that were sampled between November 2015 and October 2016. Samples were analyzed for pH, dissolved oxygen, temperature, specific conductance, nitrate + nitrite, ammonium, total nitrogen, total phosphorus, and dissolved organic carbon. Selected samples also were analyzed for gaseous concentrations of nitrogen and argon. Water-level altitudes were measured during October 24 – 26, 2016 in nine drive-point wells at three well clusters in one transect at low, high, and mean tides to determine hydraulic-head gradients. This data release includes a data file (Aggregate_Data.csv) in comma-separated values (CSV) format that includes information about each sample collection or measurement site and field and laboratory analytical data. Site information includes U.S. Geological Survey (USGS) site name, USGS 15-digit site identification number, site type, site status, location in state plane coordinates, surface elevation, measuring point heights, the depths of the bottom of the screens below land surface, altitudes of the top and bottom of the screens, mid-screen altitudes, location along the transect, tide level, and water depth, date and time sampled.