The Gemsbok Sub-basin is situated in the south-western corner of the Kalahari Karoo Basin and extends south from the Kgalagadi District of Botswana into the Northern Cape (South Africa); and west into the Aranos Basin (southeast Namibia). The Sub-basin preserves a heterogeneous succession of Upper Palaeozoic to Lower Mesozoic sedimentary and volcanic rocks of the Karoo Supergroup. Because the succession is largely covered by the Cenozoic Kalahari Group, the stratigraphy of the succession is not as well understood as the Main Karoo Basin in South Africa. Most research in the Gemsbok Sub-basin is based on borehole data. This study focuses on the intrabasinal correlation, depositional environments and provenance of the Karoo Supergroup in the Gemsbok Sub-basin in Botswana and Namibia. Based on detailed sedimentological analyses of 11 borehole cores of the Karoo Supergroup in the Gemsbok Sub-basin of Botswana and Namibia, 8 facies associations (FAs) comprising 14 lithofacies and 2 trace fossil assemblages (Cruziana and Skolithos ichnofacies) were identified. The facies associations (FA1 to FA8) correspond to the lithostratigraphic subdivisions (the Dwyka Group, Ecca Group, Beaufort equivalent Group, Lebung Group [Mosolotsane and Ntane formations] and Neu Loore Formation) of the Karoo Supergroup. Sedimentological characteristics of the identified facies associations indicate the following depositional environments: glaciomarine or glaciolacustrine (FA1, Dwyka Group), deep-water (lake or sea) (FA2, Ecca Group), prodelta (FA3, Ecca Group), delta front (FA4, Ecca Group), delta plain (FA5, Ecca Group), floodplain (probably shallow lakes) (FA6, Beaufort Group equivalent), fluvial (FA7, Mosolotsane and Neu Loore formations) and aeolian (FA8, Ntane Sandstone Formation). The Dwyka Group (FA1) forms the base of the Karoo Supergroup in the Gemsbok Subbasin and overlain by the Ecca Group deposits. Three types of deltas exist within the Ecca Group: fluvial-dominated; fluvial-wave interaction and wave-dominated deltas. The Gemsbok Sub-basin was characterised by rapid uplift and subsidence and high sediment influx during the deposition of the Ecca Group. Petrographic and geochemical analyses of the Ecca Group sandstones revealed immature arkose and subarkose type sandstones dominated by angular to subangular detrital grains, sourced from transitional continental and basement uplifted source areas. The sandstones of Ntane Sandstone Formation are classified as subarkoses and sourced from the craton interior provenances.