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The Benguela Upwelling System (BUS), located in the southeastern Atlantic Ocean, represents one of the world's most productive regions. This system is delimited to the south by the Agulhas retroflection region. The northern boundary of the BUS is, instead, represented by the Angola–Benguela Front (ABF), which is a thermal feature separating warm waters of the Angola Basin (including the South Atlantic Central Water; SACW) from the cooler Benguela Oceanic Current (BOC). We performed statistical analyses on planktonic foraminiferal assemblages in 94 samples from Holes U1575A and U1576A, cored during International Ocean Discovery Program (IODP) Expedition 391. Drilled sites are located along the Tristan–Gough–Walvis Ridge (TGW) seamount track in the northern sector of the BUS (offshore the Namibian continental margin). The analyzed stratigraphic intervals span the Early–Late Pleistocene, marked by the Early–Middle Pleistocene transition (EMPT; 1.40–0.40 Myr), during which important glacial–interglacial sea surface temperature (SST) variabilities occurred. This work provides novel insights on the local paleoceanographic evolution of the northern BUS and associated thermocline variability based on the ecological significance of the foraminiferal assemblages. Specifically, variations in the assemblage content allowed us to characterize the different water masses (BOC, SACW, and Agulhas waters) and reconstruct their interactions during the Quaternary. The interplay of the previously mentioned water masses induced perturbations in the BUS (ABF latitudinal shifts and input of tropical waters from the Agulhas retroflection region). Furthermore, we investigated the possible link between changes in the paleoceanographic conditions and climatic events (e.g., Benguela Niño-/Niña-like phases and deglaciation stages) recorded since the EMPT.