Here we present a comprehensive depth and thickness map of the main Karoo and Cape Basins using borehole and reflection seismic data. The depth to the Whitehill Formation, which is the focus of current shale gas interest within the Karoo, is also mapped. Change: The deepest part of the basin is in the south, along the northern boundary of the Cape Fold Belt (~4000 m in the southwest Karoo and ~5000 m in the southeast; ~5500 to 6000 m sediment thickness). The Whitehill Formation along this boundary reaches a depth of ~3000 m in the southwest and ~4000 m in the southeast. Limited borehole data in the southeastern Karoo show a broad deepening of the basin here compared to the southwestern Karoo. In the southeast near East London faulting has resulted in deepening of the basin close to the coast, with the Whitehill Formation deepening to over ~5000 km. Seismic and borehole data show that the Cape Supergroup pinches out below the Karoo Basin around Beaufort West and Graaff-Reinet in the southern Karoo (32.6°S for the Bokkeveld and 32.4°S for the Table Mountain Group). The Cape Supergroup reaches thicknesses of around 4 km in the south. The gravity effect of these sediments does not account for the Cape Isostatic Anomaly (CIA) in the southern part of the Karoo Basin near Willowmore and Steytlerville, i.e., an ~45 mGal Bouguer gravity low. A refraction seismic profile over the anomaly shows this region is associated with a large volume of low velocity/density shallow sediments (4.5 m/s2, 2500 kg/m3), as well as a low velocity/density anomaly associated with a normal fault and the Klein Winterhoek Thrust Fault (5.5 m/s2, 2650 kg/m3). These low density shallow sediments are explained by uplift of Karoo and Cape sediments of ~2 km or greater that is evident on Soekor reflection seismic data. This deformation has brought lower density shales (1800 to 2650 kg/m3) of the Ecca Group closer to the surface. These shallower features along with a deeper lower crust in this region (6.5 m/s2, 2900 kg/m3) are interpreted to account for the CIA.