Sound knowledge of hydrogeological setting is required for effective groundwater resource management and protection. In the basement environment where groundwater occurrence is discontinuous and highly heterogeneous, hydrogeological conceptual model is required to understand the occurrence and flow pattern of groundwater. This study presents an integrated 2D and 3D GIS method for conceptual modeling of the hydrogeological setting of a basement complex aquifer system in Osun Drainage Basin, Southwestern Nigeria. The efficiency of conjunctive use of RockWorks, Suffer and ArcGIS for surface and subsurface 3D hydrogeological modeling of a basement aquifer system was evaluated.Three distinct aquifers (Weathered Layer Aquifer (WLA), Unconfined Fractured Aquifer (UFA) and Confined Fractured Aquifer (CFA)) were delineated. WLA is characterized by low hydraulic conductivity (K = 0.34–27.54md−1, mean = 4md−1), hence low yield potential. Transmissivity (T) range and mean (0.6–1368 m2d−1, 85 m2d−1) indicate restricted flow within WLA. UFA is hydraulically connected to the underlying multi-layered CFA in the contact zones. The occurrence of UFA is localized within meta-sedimentary environment and it acts as the recharge redistributing medium, connecting the deep seated aquifers with the highly porous surface flaggy rubbles. CFA is characterized by relatively high mean K (0.2–91md−1, mean = 11md−1) and relatively high T (1.6–7185 m2d-1, mean = 483 m2d−1). Comparative analyses of aquifers’ hydraulic properties and spatial pattern of occurrence affirm that regional groundwater flow only takes place within CFA. The variation of hydraulic properties along fault lines is attributed to alternating occurrence of bedrocks of different structural and physico-chemical characteristics. Three distinct groundwater flow systems were identified in the study basin: i) the radially concentric localized shallow groundwater flow systems that occur within the overburden, ii) the W-E oriented regional flow system that feeds the source of Ikogosi Warm Spring in the adjourning basin, and iii) the NNE-SSW trans-current flow system that traverses the study basin at the center. While the first flow system is controlled by surface topography and the hydraulic properties of the vadose zone, the second and third flow systems are structurally controlled. The efficiency and efficacy of the methodology presented in this study is sufficient to develop hydrogeological conceptual model for highly heterogeneous, discontinuous basement aquifer system. Therefore, the developed conceptual model could be transformed to a numerical model of the study basin.