Successful groundwater resources evaluation and management is nowadays typically undertaken using distributed numerical groundwater flow models. Such models largely rely on hydrogeological conceptual models. The conceptual models summarize hydrogeological knowledge of an area to be modelled and thereby providing a framework for numerical model design. In this study, an efficient data integration method for developing hydrogeological conceptual model of the large and hydrogeologically-complex, Central Kalahari Basin (CKB) aquifer system, was undertaken. In that process, suitability of 3-D geological modelling with RockWorks code in iterative combination with standard GIS (ArcGIS) was tested. As a result, six hydrostratigraphic units were identified, their heads and related flow system interdependencies evaluated and hydraulic properties attached. A characteristic feature of the CKB is a thick unsaturated Kalahari Sand Unit (KSU), that restricts the erratic recharge input to <1 mm yr−1 in the centre to about 5–10 mm yr−1 in the eastern fringe. The analysis of the spatial distribution of topological surfaces of the hydrostratigraphic units and hydraulic heads of the aquifers, allowed to identify three flow systems of the three aquifers, Lebung, Ecca and Ghanzi, all three having similar radially-concentric regional groundwater flow patterns directed towards discharge area of Makgadikgadi Pans. That pattern similarity is likely due to various hydraulic interconnections, direct or through aquitard leakages, and also due to the presence of the overlying unconfined, surficial KSU, hydraulically connected with all the three aquifers, redistributing recharge into them. The proposed 3-D geological modelling with RockWorks, turned to be vital and efficient in developing hydrogeological conceptual model of a large and complex multi-layered aquifer systems. Its strength is in simplicity of operation, in conjunctive, iterative use with other software such as standard GIS and in flexibility to interface with numerical groundwater model. As a result of conceptual modelling, fully 3-d, 6 layer numerical model, with shallow, variably-saturated, unconfined layer is finally recommended as a transition from conceptual into numerical model of the CKB.