Submarine groundwater discharge (SGD) can be an important pathway for transport of nutrients and contaminants to estuaries. A better understanding of the geologic and hydrologic controls on these fluxes is critical for their estimation and management. We examined geologic features, porewater salinity, and SGD rates and patterns at an estuarine study site. Seismic data showed the existence of paleovalleys infilled with estuarine mud and peat that extend hundreds of meters offshore. A low-salinity groundwater plume beneath this low-permeability fill was mapped with continuous resistivity profiling. Extensive direct SGD measurements with seepage meters (n = 551) showed fresh groundwater discharge patterns that correlated well with shallow porewater salinity and the hydrogeophysical framework. Small-scale variability in fresh and saline discharge indicates influence of meter-scale geologic heterogeneity, while site-scale discharge patterns are evidence of the influence of the paleovalley feature. Beneath the paleovalley fill, fresh groundwater flows offshore and mixes with saltwater before discharging along paleovalley flanks. On the adjacent drowned interfluve where low-permeability fill is absent, fresh groundwater discharge is focused at the shoreline. Shallow saltwater exchange was greatest across sandy sediments and where fresh SGD was low. The geologic control of groundwater flowpaths and discharge salinity demonstrated in this work are likely to affect geochemical reactions and the chemical loads delivered by SGD to coastal surface waters. Because similar processes are likely to exist in other estuaries where drowned paleovalleys commonly cross modern shorelines, the existence and implications of complex hydrogeology are important considerations for studies of groundwater fluxes and related management decisions.