During the breakup of Gondwana the Mozambique Ridge, a Large Igneous Province emplaced between 140 and 125 Ma, was located in the evolving African–Southern Ocean gateway. Therefore, it represents an archive of the evolving exchange of water masses between the South Atlantic and Indian Ocean via the development of surface, intermediate, and bottom circulation. Two Cretaceous seismic units (S1 and S2a) were deposited on top of magmatic basement separated by a hiatus. Unit S1 mostly shows seismic reflections parallel to the top of the basement and no indications of current activity. The occurrence of several sediment drifts within seismic unit S2a indicates the onset of current controlled sedimentation. Based on our observations we propose deposition under partly euxinic conditions in the area of the Mozambique Ridge until ~ 100 Ma. The onset of a strong shallow circulation affecting deposition at the Mozambique Ridge is inferred by the Late Cretaceous ~ 25 Myr hiatus reported by drilling results and documented in the seismic records, whereas black shales deposited in the nearby deep Transkei Basin indicate a restricted deep circulation at least until ~ 85–80 Ma. We propose that the observed hiatus might be a consequence of a late Early Cretaceous uplift of the Mozambique Ridge and the progressive opening of the Agulhas Passage allowing inflow of surface (Upper Pacific Water, Upper North Atlantic Water) and intermediate water (Intermediate Southern Ocean Water) into the study area. The intense circulation that caused the hiatus seems to have weakened in Campanian times, which is documented by the occurrence of sediment drifts in seismic unit S2a. We suggest that the onset of current controlled sedimentation was caused by palaeogeographic modifications in the Atlantic Ocean along with relocation of circulation pathways. Our results illustrate the crucial role of the African–Southern Ocean gateway in the commencing water mass exchange between the Atlantic and Indian Ocean and highlight the complex interactions that eventually lead to the initiation of a proto–Antarctic Circumpolar Current in Turonian times.