The region south of South Africa is unique for studying the development of thermohaline circulations. We observe strong bottom currents, such as North Atlantic Deep Water (NADW) and Antarctic Bottom Water (AABW) that meet south west off South Africa and flow eastward through the Transkei Basin into the Indic. Due to their high sedimentary freight, they are the most important source for the Transkei Basin infill. The analysis of this infill gives evidence for strong bottom current activity in this region since at least late Eocene times. Newly collected high resolution seismic reflection data reveal recurrent changes in AABW and NADW flow paths and strengths that can be directly linked to large scale events, such as the opening of the Drake Passage for deep water or the closure of the Isthmus of Panama. Additionally, we observe two large sediment drifts in the basins centre which mirror stable deep sea current conditions over a long period of time. We analysed the Transkei Basin infill and produced a depositional model for the past 90 Ma. Consequentially, we reconstructed the bottom current development south of South Africa since late Eocene times.