Large-scale irrigational schemes have drastically reduced the surface water discharge into the Aral Sea, causing a sea surface level lowering of more than 20 m since 1960 and severe water quality deterioration in the region. We investigate the dynamics of submarine groundwater discharge (SGD) into the Aral Sea as well as the saltwater intrusion (SWI) into the coastal groundwater around the Aral Sea during its shrinkage by using the U.S. Geological Survey SUTRA code. Results show that the regional topography and bathymetry largely influence SGD and SWI transients as the Aral Sea shrinks. Considering the flat conditions that prevail in the southeastern Aral Sea and the irrigated Amu Darya delta, SGD drops as the sea starts to shrink because the shoreline displacement prevents seawater inflow to the aquifer and subsequent return flow to the sea. In this flat bathymetry case the groundwater discharging into the Aral Sea becomes as saline as the seawater because saltwater remains below the dried seabed. In contrast, for the steep bathymetry of the essentially uninhabited northwestern region the SGD increases as a combined effect of sea surface lowering, density differences, and storage, with the SGD salinity remaining below seawater salinity and reflecting a considerable freshwater component. Considering the potential for groundwater pumping in the original coastline vicinity for freshwater supply use, our results indicate a decreased risk of SWI in the northwestern Aral Sea region under the post-1960 sea level lowering conditions.