An analysis of borehole logs with hydrophysical data from the Lagos coastal belt, Southwestern Nigeria, was carried out to evaluate the subsurface lithological units and geo-environmental impact of seawater intrusion into coastal freshwater. Forty-five (45) borehole logs, consisting of natural gamma, electrical resistivity log and hydrophysical parameters were integrated to delineate saline and fresh aquifer zones and propose simplified conceptual models for adequate groundwater characterisation and development. The qualitative interpretation of the borehole logs revealed a complex lithology of alternating sequences of sand and clay layers. The study also showed that the subsurface was variably intruded by saline water indicated by low resistivity values with freshwater/saline water boundaries occurrence at depths ranging between 14 and 157 m from west to east. The variation in depths of occurrence of freshwater/saline water interface is dependent principally on the proximity to saline/brackish water source as well as variation in lithology. Complementarily, the average electrical conductivity (EC) of 1770 μS/cm (GW1–7) and 1676 μS/cm (GW8–13) recorded in groundwater at Apapa in the west and Island at the central part, respectively, further confirmed saline incursion of the coastal aquifers in the region. This study demonstrates versatility of geophysical borehole logs in identification and differentiation of the subsurface lithology and its fluid content.