Offshore freshened groundwater (OFG) is a potential unconventional water source for coastal cities, but its spatial distribution, emplacement mechanisms and the geological factors influencing OFG migration and preservation remain poorly constrained. The Gulf of Corinth (GOC) in Greece, an active continental rift, presents a unique study area where pore-water freshening has been documented through scientific drilling. In this study, the spatial distribution, emplacement mechanisms and controls on OFG has been investigated in the GOC sediments by integrating core physical properties, lithostratigraphy, 2D seismic reflection data and 2D hydrogeological modelling. The freshened water extends from ca. 20 to 600–700 m below seafloor (mbsf) in the central subbasin and from ca. 15 to 150 mbsf in the eastern subbasin of the Alkyonides Gulf. This freshened water in the gulf sediments is attributed to meteoric recharge during glacial periods. A 2D hydrogeological model of salinity changes over the past 800,000 years confirms that the deep basin’s freshened water is a remnant from sea-level lowstands. The results indicate that both glacial and interglacial sediments stored freshwater, with salinity variations occurring independently of total porosity, likely because of vertical diffusion of fluids across sediments deposited during multiple interglacial and glacial cycles. The laterally continuous seismic units in the gulf basin may contain up to 250 km3 of freshened groundwater. This study offers new insights into the occurrence and distribution of freshened groundwater in rift basins, highlighting the role of long-term sea-level fluctuations in groundwater freshening, and providing a comprehensive model for groundwater storage capacity in such environments.