Several large Holocene paleochannels were mapped using subsurface high-resolution seismic reflection profiles under the Inland Bays of Delaware, a shallow coastal estuary system along the Mid-Atlantic Coast. Low-permeability fill of the paleochannels may serve as a quasi-vertical aquitard that forces groundwater from deep flow paths to discharge upward into the bays. The hypothesis that these channels control the locations of offshore ground-water discharge is being tested by comparing results of this seismic survey with results from thermal-infrared imaging, electrical resistivity surveys, and pore-water sampling. This work is part of an EPA-funded CISNet (Coastal Intensive Sites Network) project entitled “CISNet: Nutrient Inputs as a Stressor and Net Nutrient Flux as an Indicator of Stress Response in Delaware’s Inland Bays Ecosystem.” Approximately 200 km of seismic profiles were obtained using an Edgetech CHIRP 2-12 KHz-frequency acoustic sub-bottom profiler with decimeter-scale vertical resolution. In the shallow waters of the Inland Bays (depths of 1-4 m), the CHIRP 216S-towfish was suspended at depths of 1 m beneath the water surface through the center-opening of a modified pontoon craft. The seismic data were correlated with more than 120 existing cores from the bays. The CHIRP profiles show strong reflections associated with the boundary of Holocene fine-grained sediments with pre-Holocene sand and also within Holocene sedimentary units (e.g., lagoonal sediments vs. marsh mud). Some of the fine-grained organic sediments that fill the paleochannels appear to be undergoing bacterial decomposition, producing methane and other free gases. The subsurface stratigraphy, including the geometry of the paleochannels, are poorly resolved below the strong reflections associated with the presence of gas. Beneath Rehoboth Bay, two major paleochannels trend toward the south-east where they combine into a single channel that can be traced beneath the present day barrier island and the floor of the Atlantic Ocean. A single, major paleochannel beneath Indian River Bay can be traced beneath the Indian River Inlet also extending toward the east below the floor of the Atlantic Ocean.