Population pressure, recent droughts and sea-level rise associated with climate change projections increase pressure on secure water resources, notably on groundwater of the coastal areas like Maputo, Mozambique. The Matola River, located in the west of Maputo, is a perennial river that consists of mostly brackish/salt water originating from groundwater seepage and salinity makes the river water unusable. The main source of the saline groundwater is assumed to be fossil seawater, entrapped in the silty marl and clay dominated aquitard. However, detailed studies about the salinity problem of coastal Maputo city, particularly of Matola River is very limited. This research focuses on the integration of regional hydrogeochemistry, isotopic analysis, and groundwater flow models to trace the source of saltwater and to improve the management of water resources in Matola wetlands. The hydrogeochemical analyses of major ions will reveal the prominent hydrochemical processes responsible for the evolution of groundwater. Water stable isotopes (δ2H, δ18O) results will validate the sources of salinity and mixing processes. Using the result of 13C/14C (DIC) and 36Cl/Cl isotopes, the study aims to calibrate the residence time and flow paths of the already existing groundwater flow and salt transport models for testing the mentioned hypothesis. Based on the overall findings, some adaptation measures will be proposed to cope with the saline groundwater. Investigating the origin of salinity and proposing measures are expected to help in the domestic supply and crop productivity sectors of Matola River adjacent areas. It can also assist the policymakers to take feasible solutions to sustainable groundwater management.