High-resolution marine seismic reflection and ground penetrating radar (GPR) methods were used to place constraints on the hydrostratigraphy of Delaware's Inland Bays. As part of an integrative study to determine the net fluxes of nutrients into estuary systems, these geophysical techniques were employed to investigate groundwater discharge into the bays and their adjoining creeks. This work was part of an EPA-funded Coastal Intensive Sites Network project entitled: CISNet: Nutrient Input as a Stressor and Net Nutrient Flux as an Indicator of Stress Response in Delaware's Inland Bays Ecosystem. An Edgetech CHIRP sonar system with decimeter-scale vertical resolution with sub-bottom penetration depths to 6-8 meters was used to collect over 200 km of profiles within Rehoboth and Indian River Bays. These profiles imaged, and further defined, paleochannel networks that had been initially identified through intensive vibracoring studies. The low-permeability sediments infilling the paleochannels may serve as quasi-vertical aquitards that may force ground water from deeper flow paths to discharge upward into the bays. At selected sites, the CHIRP results were integrated with on-land GPR profiles to investigate the subsurface stratigraphy where groundwater discharge at/near bay or adjoining creek shorelines was observed. A Sensors & Software PulseEKKO 100 system with 50 and 100 MHz antennas was used to collect the GPR data at a decimeter-scale vertical resolution with penetration depths to 6 to 10 meters beneath the subsurface.