This study investigates potential groundwater contamination near a waste disposal site in southwestern Nigeria. The area's complex geological setting, characterized by fractured rock formations, posed significant challenges for traditional monitoring methods. To address these challenges and comprehensively assess groundwater conditions, we employed a combined approach utilizing Electrical Resistivity Tomography (ERT), Ground Penetrating Radar (GPR), and geochemical analysis of heavy metals and water conductivity. This approach enabled the investigation of groundwater levels, identification of potential contamination zones, and delineation of contaminant flow paths. GPR identified a shallow zone, termed the “shadow zone,” with conductive residues indicating contaminants with anomalous conductivity ranging from 1 to 1.5 m. An intermittent reflection zone at a depth of 1.5–3.5 m suggested the potential presence of leachate-impacted groundwater. ERT confirmed a shallow resistive layer at depths of 0–2 m, attributed to compacted waste and topsoil, around the abandoned main dumpsite. Below this layer, a zone of low resistivity, decreasing downward through a porous weathered zone, was observed. This corresponded to high water conductivity in well data, ranging from 21 to 147 mS/m (equivalent to 6.80 to 47.62 Ω-m), indicating a high conductive anomaly suspected to be a leachate plume at depths of 2–10 m in a sandy-gravelly weathered zone. Validation against ground truth data confirmed the correlation between radar signatures, geoelectrical imaging, and subsurface lithology. Analysis of well and soil samples revealed concerningly elevated concentrations of cadmium, mercury, lead, arsenic, and cobalt, ranging from 641 to 1175 ppb, exceeding established safety limits for drinking water. Additionally, soil samples showed elevated levels of nickel and chromium, generally ranging from <0 to <1 ppb. These findings highlight the significant risk of groundwater contamination due to the proximity of the leachate zone to the groundwater table in the weathered basement complex. This study demonstrates the effective integration of geophysical and geochemical methods for comprehensive mapping of contaminated zones and identification of preferential pathways for contaminant migration. The findings underscore the critical need for implementing comprehensive risk assessment methodologies in similar complex geological settings.