Salty and brackish groundwater has been observed at least 100 km inland in some aquifers contained within Quaternary delta plains. This phenomenon limits access to fresh groundwater resources, particularly in the densely populated deltas of Southeast Asia. However, the causes of inland salinity are unclear. Here we present borehole and geophysical data that show that in the Red River delta plain of Vietnam, salty and brackish groundwater primarily occurs in incised valleys that were formed during sea-level lowstands during the Pleistocene. During the mid-Holocene, these valleys were filled with fine-grained marine deposits containing trapped seawater. We conduct groundwater flow simulations that show that the age, thickness, and permeability of the marine sediments are the primary controls on the leaching of salty porewater into the freshwater aquifer. We find that salty groundwater originating from this trapped seawater is still present in Holocene-aged sediments with low permeability, and affects groundwater salinity in adjacent aquifers. In contrast, trapped seawater from all Pleistocene-aged sediments has been leached. We identify a number of brackish to saline delta aquifers elsewhere in Asia and throughout the world that have a similar sedimentary history, and thus are likely to be influenced by this leaching process.