The spatial variations in Quaternary sediments on the inner continental shelf are produced by the progression of depositional environments during the latest sea-level rise, and this sedimentary architecture plays a fundamental role in controlling groundwater discharge. However, coincident seismic mapping, sediment cores, and hydrological studies are rare. Here, we combine high-resolution, 0.5–10 kHz, high-frequency seismic profiles with sediment cores to examine the nature of the sediment deposits, including paleochannels, where submarine groundwater discharge has also been studied in a 150 km2 area of the inner shelf north of Charleston, South Carolina. We used high-frequency seismic reflection to interpret seismic facies boundaries, including 16 paleochannel crossings, to 20 km offshore. From 13 vibracores taken at the intersections of the seismic lines, we defined seven lithofacies representative of specific depositional environments. The paleochannels that we cored contain thick layers of structureless mud sometimes interbedded with silt, and mud is common in several of the nearshore cores. Our results indicate that paleochannels are often mud-lined or filled in this area and were most likely former estuarine channels. Neither the paleochannels nor a mud layer were found farther than 11 km off the present shoreline. This offshore distance coincides with the strongest pulses of groundwater discharge, emerging just beyond the paleochannels. This suggests that the muddy paleochannel system acts as a confining layer for submarine groundwater flow.