The South African Gateway is a critical region for the water mass exchange between the Atlantic and the Indian Ocean. The variability in the interoceanic exchange is relevant to global climate change. High resolution seismic reflection data were collected in the Transkei Basin during R/V SONNE cruise SO–182 in 2005. These seismic observations have indicated that a large elongate mounded contourite drift, the Agulhas Drift, has been built up by eastward flows of Antarctic Bottom Water (AABW) and North Atlantic Deep Water (NADW) since about 3 Ma. For a better understanding of the influences of the various currents on sediment transport patterns in the vicinity of the Agulhas Drift, the Regional Oceanic Modeling System (ROMS) has been used to simulate the current system and suspended sediment transport processes. The results from current system simulation showed that a recurrent individual cyclonic eddy event is the key hydrodynamic feature in the Transkei Basin. These eddies are almost fixed in the center of the Transkei Basin and spread over the entire water column. Flow in their northern segments is eastward across the southern flank of the Agulhas Drift. These eddies are supposedly the result of perturbations in the Subtropical Convergence (STC) in the region of south of Africa, where planetary waves on the STC deform. The perturbations enhance the surface eddy kinetic energy (EKE) in the Transkei Basin. The high EKE is then transferred from the surface to the deep ocean, where it causes the formation of eddies at abyssal depth. Based on the ocean circulation simulations, grain size experiments were carried out to test the transport behaviors for 4 different silt grain size classes. Our simulations reveal that sediment transport patterns in the Transkei Basin are strongly influenced by the mesoscale eddies. During eddy events, silts at all tested grain sizes can be resuspended by the AABW along the northeastern flank of the Agulhas Plateau that borders the Transkei Bsin to the east, whereas not all of them can be further transported into the region of the Agulhas Drift. Coarse silt cannot be transported over long distances, but it is deposited in the vicinity of the resuspension area. Medium silt can be transported into this region of the Agulhas Drift, only when the eddy current is strong enough. Fine silt and very fine silt can easily be carried into the drift area. The simulations show that medium and fine silt can be deposited on the Agulhas Drift, whereas very fine silt is further transported out of the area into the southern Transkei Basin.