In this integrated study of seismostratigraphy and palynology we provide an insight into the depositional environment in the northern Cape Basin during the late Pliocene with respect to global climate changes. A well-pronounced succession of continuous high-amplitude reflectors characterizes the upper acoustic units off the coast of Southwest Africa. Among the seismic structures, unconformity NCB-B dated at 2.1 Ma represents a striking feature. The internal reflectors below in unit NCB-1c show toplap termination indicating stagnating deposition. In contrast, the reflectors above in unit NCB-1b onlap onto this interface, thus suggesting the return of a gentle increase in deposition. The observed reflector configurations and shifts in the location of the deposition centre correspond to a number of global and local events. The change from toplap to onlap reflector configuration corresponds to a transgressive period in eustatic sea level. Furthermore, the formation of unit NCB-1b coincides with a marked change of pollen assemblages indicating an intensified aridification of the Namibian hinterland and a loss of river discharge into the northern Cape Basin at about 2.1 Ma. Further, the onlap configuration of reflectors indicates an enhanced production and deposition, probably due to increased upwelling and an extension of upwelling filaments further seawards associated with enhanced wind stress as a result of intensification of Northern Hemisphere Glaciation. In summary, the seismic reflection pattern evidences a pronounced and sudden change of the deposition system in the latest Pliocene. Another marked climate step probably led to changes in composition and manner of transport of matter to the Cape Basin. © 2008 Elsevier B.V. All rights reserved.