The rate and pattern of groundwater discharge to a shallow coastal embayment was found to be very dynamic, being modified by short-term changes in upland hydrologic processes, fluctuations in the hydraulics of the receiving waters, and long-term changes due to depositional processes within the tidal basin. The regional and embayment morphology resulting from deglaciation and subsequent depositional processes within the aquatic system were found to be major factors affecting current patterns of groundwater discharge. Discharge through the embayment bottom based upon measured profiles of interstitial salinity, temperature, and porosity indicated that fine-grained, subtidal sediments (> 1 m thick) had low hydraulic conductivities and acted as aquicludes, limiting seepage to the marginal nearshore zone. The hydraulic gradients determining groundwater discharge to embayment waters were coupled to tidal elevations, generating periodic increases or decreases in rates of freshwater inflow. Water table maps and interstitial salinity profiles indicated that as mean tidal levels increased, groundwater discharge decreased, and conversely at low mean tide levels discharge into the embayment increased. During peak embayment levels the embayment acted like a flow-through lake with groundwater discharging along one shore while saline embayment waters simultaneously infiltrated along the opposite shore. Simultaneously, upland groundwater flow diverged from the embayment, resulting in significant reduction (29%) in the area contributing groundwater to the embayment. Changes in the patterns and rates of groundwater discharge, due to seasonal variations in water table elevation or short-term variations in embayment level, underscore the need to integrate upland water table mapping with hydraulic measurements within the zone of discharge when estimating the input of groundwater and groundwater-borne nutrients to coastal embayments.