The Benguela Upwelling System (BUS) exerts a major oceanographic and sedimentary influence on the Namibian and western South African continental margin. Previous literature has distinguished between the Northern Benguela Region (NBR) and Southern Benguela Region (SBR) due to the varying sedimentary, oceanographic, upwelling and faunal nature of the two areas. A comprehensive understanding of how upwelling and palaeoceanography between these two subsystems relate to, or differ between each other, is limited. Late Quaternary foraminifera are extremely useful in recording and tracking past oceanographic and climatic changes in the region. Planktic foraminifera from two cores recovered from the western continental slope of South Africa, at a water depth of ∼3500 m, were analysed and compared to previous studies from the region to determine any variations in the water mass, oxygenation, upwelling and productivity history between the NBR and SBR, and during glacial-interglacial periods. Results from this study indicate that influence from subpolar, subtropical and upwelled surface waters play a major role in the faunal distributions and oceanographic history of the area. Abundances of subpolar species are lowest off western South Africa during interglacial periods, indicating obstruction from the subtropical convergence and restriction of the polar fronts during those periods. Benthic and planktic foraminifera indicate strengthened upwelling and the extension of upwelling cells further slopeward during glacial periods. Increased productivity associated with stronger upwelling during glacial periods led to increased nutrient and organic matter delivery to the seafloor, resulting in eutrophic conditions. These environments are further amplified by nutrient-rich bottom water masses that are strengthened during these periods. Upwelling intensity and productivity also exert controls on the benthic foraminifera, where epifaunal taxa abundances and epifaunal-infaunal ratios increase from the NBR to SBR, and glacial epifaunal-infaunal ratios decrease compared to interglacial periods. Higher abundances of tropical-subtropical species were recorded in the NBR and Agulhas retroflection relative to western South Africa, indicative of the influence of the Angola-Benguela Front to the north of upwelling zones and the inflow of warm Agulhas Current waters from the South Indian Ocean to the southwest of South Africa. This study therefore reveals that the NBR and SBR vary in their palaeoceanographic record as a result of their position to important southeast Atlantic oceanographic features such as the Angola-Benguela Front, the Agulhas Current, the Benguela Current and polar fronts.