Aquifers adjoining tropical oceans, such as the Ganges-Brahmaputra-Meghna river fluvio-deltaic system, host > 30% of the global population, highlighting the importance of understanding their geochemical signatures and the processes governing them. Here, Sr signature has been used as a conservative geochemical tracer together with some other major ions to delineate the hydrological processes and salinisation of groundwater by exchange with surface water (sea, river, and tidal creeks) and multi-depth groundwater in and around the Ganga River mega-delta. Our study results revealed that there are significant differences between the studied hydrological reservoirs and a change in lithological and hydrogeochemical conditions reflects changes in sediment source and dominant geochemical processes. An increasing rate of chemical weathering is observed within the delta system for river water. Similarly, Sr values are indicative of higher interaction of groundwater with aquifer sediment, which suggests a longer residence time observed in inland parts of the basin. Silicate weathering with minor carbonate weathering is the dominant process regulating the Sr cycling between lithologic and hydrologic reservoirs within the basin. In contrast, the groundwater Sr in coastal, delta-front aquifer systems is dominantly influenced by exchanges with seawater. The intruded brackish water mixes with resident fresh groundwater and is discharged into the coastal ocean as submarine groundwater discharge.