Geologically complex crystalline aquifers are distributed extensively in Africa and also underlie large parts of the semi-arid Limpopo Province where some of the greatest groundwater needs in South Africa occur. The importance of these basement aquifers makes it vital to identify high yielding hydrogeological zones that can be targeted for water supply, to sustain areas of high population density with few or no alternative water sources. The biggest challenge is to understand the factors that determine the secondary permeability of these weathered-fractured rock aquifers. The focus of this study was therefore to systematically analyse regional factors that may influence borehole yields and aquifer transmissivities. The study covered four distinct geological and morpho-structural domains within the Limpopo Province, covering about 23 500 km2. The borehole dataset compiled for the study consisted of over 8 000 boreholes contained in the Groundwater Resources Information Project (GRIP) Limpopo database of the South African Department of Water Affairs. Approximately 3 000 of these boreholes have been hydraulically tested and the lithology has been recorded in 1 200 cases. A commonly encountered problem of pumping tests analysis in crystalline aquifers is in choosing an appropriate model that best fits the observed drawdown response. In this thesis modern methods are proposed for the analysis of pumping test data in weathered-fractured rock aquifers and highlight the importance of diagnostic plots, especially derivatives, for the detection of flow regimes and the choice of the correct ‘theoretical’ model. Based on the classification no single analytical method can be universally applied to crystalline basement aquifers when considering the analysis of pumping test data. The GRIP borehole dataset was analysed in conjunction with spatial information to identify the relationship of regional factors such as - geology, hydrology, weathering thickness, topography, geomorphology, neo-tectonic stresses, and structural lineaments - on groundwater occurrence. Geology has a clear influence, with boreholes exploiting alluvial aquifers composed of highly permeable material, and certain rock types such as pegmatite, showing generally higher borehole productivities. Favourable borehole locations from a topographical point of view are predictably along rivers and valleys. Other identified favourable groundwater targets are the metamorphic aureoles of younger granite intrusions. Despite the local importance of the regolith as a recharge and storage mechanism for the underlying fractured bedrock, no correlation between borehole yields and depth of weathering was found. The pattern of lineament and dyke orientations in the different morpho-structural domains led to a more complex conceptual model of groundwater occurrence. This model is inconsistent with the predicted regime based on regional stress field data and suggests that local variations have a strong influence on groundwater occurrence. Due to the complex geological history of the area, it is difficult to link open discontinuities to a distinct recent or past tectonic event. It can be concluded that regional stress field data, as in this case, may not account for local, possibly highly significant, stress field variations. The hydrogeological importance of several factors on groundwater occurrence presented in this study can be used as a working reference for future groundwater development programmes.