Abstract: Groundwater and surface water in Souss–Massa basin in the west-southern part of Morocco is characterized by a large variation in salinity, up to levels of 37gL−1. The high salinity coupled with groundwater level decline pose serious problems for current irrigation and domestic water supplies as well as future exploitation. A combined hydrogeologic and isotopic investigation using several chemical and isotopic tracers such as Br/Cl, δ18O, δ2H, 3H, 87Sr/86Sr, δ11B, and 14C was carried out in order to determine the sources of water recharge to the aquifer, the origin of salinity, and the residence time of water. Stable isotope, 3H and 14C data indicate that the high Atlas mountains in the northern margin of the Souss–Massa basin with high rainfall and low δ18O and δ2H values (−6 to −8‰ and −36 to −50‰) is currently constitute the major source of recharge to the Souss–Massa shallow aquifer, particularly along the eastern part of the basin. Localized stable isotope enrichments offset meteoric isotopic signature and are associated with high nitrate concentrations, which infer water recycling via water agricultural return flows. The 3H and 14C data suggest that the residence time of water in the western part of the basin is in the order of several thousands of years; hence old water is mined, particularly in the coastal areas. The multiple isotope analyses and chemical tracing of groundwater from the basin reveal that seawater intrusion is just one of multiple salinity sources that affect the quality of groundwater in the Souss–Massa aquifer. We differentiate between modern seawater intrusion, salinization by remnants of seawater entrapped in the middle Souss plains, recharge of nitrate-rich agricultural return flow, and dissolution of evaporate rocks (gypsum and halite minerals) along the outcrops of the high Atlas mountains. The data generated in this study provide the framework for a comprehensive management plan in which water exploitation should shift toward the eastern part of the basin where current recharge occurs with young and high quality groundwater. In contrast, we argued that the heavily exploited aquifer along the coastal areas is more vulnerable given the relatively longer residence time of the water and salinization processes in this part of the aquifer.