Application of regional geophysical methods for hydrogeological purposes has increased over the last two decades especially in arid and semi-arid areas. A project to map the Kraaipan granite-greenstone terrain in southeast Botswana has recently been undertaken using regional aeromagnetic and gravity data with the aim to map the rocks at depth to understand the geology while the secondary objective was to subsequently assess the mineralization and groundwater potential in the area. An integrated analysis of the aeromagnetic and gravity data and their derived/processed products is hereby investigated for groundwater for drinking and agricultural purposes. The studies include: subsurface characterisation and delineation of structural framework suitable for groundwater exploration and determination of petrophysical relationships used to link the geophysical properties (e.g., density) to hydrological properties (e.g., porosity). The results of interpretation indicate that the rocks are under ~50 m of Kalahari cover and the study area is composed of three aquifers: the extensive hard rock aquifer (granitic and volcanic), the important (fractured) karst aquifer and the minor sedimentary aquifer. The area is dissected by an ENE-to-EW-trending dyke swarm visible on the regional aeromagnetic data and much clearer on high resolution aeromagnetic data. Minor fault and/or dyke elements of NW-SE and NE-SW trend are observed. Spectral analysis reveals three main average ensample interfaces at depths of 0.7 km, 1.99 km and 4.8 km. The linear Euler solutions maps reveal that the majority depths to top of magnetic bodies range from 40 m to 400 m throughout the survey area. The shallowest depths are the most significant one in this case as they probably relate to depth of bedrock and thickness of regolith or thickest sediments. For 2695 existing boreholes analysed, maximum borehole depth is 482 m (mean 108 m), and almost half (1263) /hr) and an average water strike of 64 m. There is very little correlation between interpreted hydrogeological features and the existing borehole locations. The study shows the importance of preliminary geophysical investigations before ground borehole siting and drilling in order to improve borehole success rates and/or reduce costs inherent in groundwater projects.