Weeks Bay is a small estuary located on the U.S. Gulf Coast which drains approximately 520 square kilometers of predominantly agricultural land in Baldwin County, Alabama. A two-year hydrogeological investigation of the bay focused on detecting and quantifying groundwater discharges into the bay, measuring the amount of dissolved inorganic nitrogen delivered to the bay via groundwater, and delineating of nitrogen fate and transport along influent groundwater flow paths. The work involved the installation and quarterly monitoring of several offshore piezometers and onshore monitoring wells, and found that groundwater contributes, on average, about 30,000 cubic meters of freshwater to Weeks Bay each day (about 4 percent of the overall riverine input). Groundwater discharges into the bay from two aquifers: a shallow water-table aquifer that is in direct hydraulic contact with Weeks Bay, and a deeper, confined aquifer that is separated from the bay by a confining unit. This confining unit includes extremely low-permeability sediments situated along the bay bottom. Nitrogen concentrations detected in groundwater displayed a great degree of seasonal variability but showed a trend of increasing nitrate and decreasing ammonium with depth. Nitrate reduction occurs as groundwater flow paths pass through anoxic sediments in the bay and the riparian zone. Peak nitrate concentrations detected occasionally in bay waters could not be correlated to groundwater influx, but there is evidence that day-to-day nitrate concentrations in the water column are similar to those detected in submarine groundwater discharges.