Knowledge of coastal groundwater flow is critical for managing coastal groundwater resources and quantifying submarine groundwater discharge (SGD), but this flow occurs over multiple scales that can be difficult to study in an integrated way. We designed a field and modeling study to investigate groundwater flow and the distribution of salinity during sea level rise in a domain that included beaches, salt marshes and the first major confined aquifer, which reached 10-15 km offshore. Numerical models were based on the flat-lying, passive margin coastline of North Inlet, SC, and were constrained by field studies including subsurface resistivity surveys and hydraulic head observations. Simulations that included tidal fluctuations showed that the salt marsh generated more than three times as much SGD as the beach and inner shelf, per unit length of coastline. Groundwater exchange between scales was small, suggesting that physical fluxes of groundwater can be considered independently at different scales. However, salinization of the first major confined aquifer occurred by downward transport from overlying aquifers rather than intrusion from the seaward end, suggesting that studies of aquifer salinization should consider multiscale flow. During simulated sea level rise, fresh-to-brackish groundwater persisted in the first confined aquifer as far as the seaward end of the overlying confining unit, 10-20 km offshore. Total fluxes of SGD decreased significantly with future sea level rise, dominated by declining SGD in the salt marsh, and portending a marked decline in the flux of nutrients and carbon to estuaries and the coastal ocean. Plain Language Summary Knowledge of groundwater flow and transport in coastal areas is critical for managing water resources and for understanding the delivery of solutes to the ocean. Groundwater flow in coastal areas occurs at many spatial scales, but it has been difficult to judge the relative importance of flow at different scales. It has also been difficult to map the transition from fresh to salty groundwater. Our work compares groundwater flow at different scales to investigate controls on the freshwater-saltwater interface in three stacked coastal aquifers in South Carolina. In simulations, confined aquifers can retain fresh water very near the seafloor 10 km offshore, if the aquifer is protected by a dense mud layer. The aquifer may not be entirely fresh between land and the seafloor, however. Salt can diffuse across confining layers into deeper aquifers. Fresh and saline groundwater also carry important dissolved constituents to the ocean. We found that the volume of groundwater discharge from salt marshes was much larger than discharge from the seafloor, suggesting that future studies should focus on salt marshes. Sea level rise will likely drown the marsh over the next 100 years, and the volume of groundwater that flows to the ocean will decline.