Abstract The Kalahari Copperbelt in northwestern Botswana is characterized by structurally controlled, stratabound, mineralogically zoned copper-silver deposits hosted along a major redox boundary within a late Mesoproterozoic rift succession. Copper-silver mineralized rocks occur on the limbs and in the hinge positions of regional-scale folds that characterize the Pan-African Ghanzi-Chobe zone fold-and-thrust belt. Regional facies changes along the base of the transgressive marine D’Kar Formation, the host to the majority of mineralized rocks, delineate a series of synsedimentary basin highs and lows. The facies changes were identified through both lithostratigraphic analysis of drill holes and along-strike variations in magnetic lithostratigraphy, a technique that correlates the magnetic fabrics of second vertical derivative aeromagnetic maps with changes in lithostratigraphy. Basin highs controlled the development and distribution of favorable lithostratigraphic and lithogeochemical trap sites for later sulfide precipitation. Major facies changes across the Ghanzi Ridge area straddle a significant crustal structure identified in gravity datasets that appears to have influenced extensional activity during basin development. During basin inversion, the basin highs, cored by rheologically stronger bimodal volcanic rocks, localized strain within mechanically weaker rock types of the Ghanzi Group metasedimentary rocks, leading to the development of locally significant permeability and the formation of structural trap sites for mineralization by hot (250°–300°C), oxidizing, metalliferous Na-Ca-Cl brines. Structural permeability was maintained within trap sites due to silicification and/or feldspar alteration during progressive deformation and associated hydrothermal mineralizing events.