In the crystalline basement terrains of Southwestern Nigeria, groundwater exploration remains a significant challenge due to the extreme lateral and vertical heterogeneity of the subsurface. This study investigates the Agbaje–Ijokodo area in Ibadan, a region historically plagued by high borehole failure rates, using an integrated geophysical approach. By combining 1D Vertical Electrical Sounding (VES) at 28 locations with 2D Electrical Resistivity Tomography (ERT) across 14 profiles, we mapped the complex architecture of the local aquifer system. The results reveal a predominant three-layer geoelectric sequence: a clayey topsoil, a weathered saprolite layer (averaging 10.8 m in thickness), and a basal fractured-to-fresh basement. Interpretation of geoelectric curves, primarily H-type (57%) and Dar-Zarrouk parameters indicates that while the weathered regolith provides storage, its productivity is often hampered by high clay content. Critical secondary porosity was identified in deep-seated fracture zones and basement depressions, particularly in the Agbaje sector, where reflection coefficients below 0.75 and longitudinal conductance values (0.2 - 0.69 mhos) suggest both high groundwater potential and moderate protective capacity. In contrast, the Ijokodo area is characterized by shallow bedrock ridges and thin overburden, explaining its poor-to-fair yield history. These findings suggest that sustainable groundwater development in the area must shift from targeting shallow saprolite to deeper, localized fracture networks. This research demonstrates that an integrated resistivity framework is indispensable for reducing the risks associated with borehole siting in complex metamorphic terrains.