Knowledge of the source of water in the Lagos coastal basin (LCB) groundwater system was to be found vital to the future development and management of the system. Stable and radioactive isotopic measurements have been employed to unravel the source of recharge and residence time of the shallow groundwater system, based on the sampling conducted in 2016 and 2017 on groundwater, surface water and rainfall. The concentration of tritium in the groundwater samples were very low and ranged from less than 1 to 2.8 TU, while measured 14C contents ranged from 59.1 to 88 pMC. The δ18O values of groundwater samples ranged from 4.81 and 3.98 ‰, while the δ2H values ranged from -24.75 and -19.70 ‰ for the wet and dry seasons, respectively. The obtained results indicated non-existence of paleo recharge; rather all groundwater in the basin were found to be essentially of meteoric origin with intermittent surface water contributions. Moreover, shallow groundwater and surface water have considerable variations in isotopic compositions, reflecting evaporation and preservation of seasonal fluctuation. Though there was an observed generally low tritium content, however, it proved useful in the identification of recent active recharge taking place across the basin. The deduced radiocarbon age reflected the presence of “modern water” and thus supports the presence of present recharge to the groundwater system. Therefore, the source of the shallow groundwater recharge was actively renewable particularly during the wet season and thus water exploitation is potentially sustainable in the basin.