The Indian-Atlantic Ocean Gateway significantly modulates thermohaline circulation and impacts the Atlantic Meridional Overturning Circulation (AMOC). Site U1479 in the Cape Basin, recovered during International Ocean Discovery Program Expedition 361, lies at the transition between the Benguela and Agulhas currents, recording interactions between the Indian, Atlantic, and Southern oceans during major climate transitions. We use absolute diatom abundance (ADA), diatom assemblage groups, and high-resolution biogenic silica and sediment geochemistry to evaluate sea-level change, ocean frontal migrations, and water-mass variability in the southeastern Cape Basin from 1,050 to 440 ka. Diatom reconstructions reveal a three-step shift in abundance, assemblage, and preservation across the Mid-Pleistocene Transition (MPT). From Marine Isotope Stage 23 to 12, the record captures evolving southern sourced water transport and upwelling, alongside a southward expansion of the Benguela Upwelling Zone. The data are consistent with paleoclimate evidence for glacial equatorward displacements of Southern Ocean fronts by roughly 5 to 7° latitude during the MPT, altering Agulhas Leakage, with significant implications for the AMOC. Elemental geochemistry, together with ADA and assemblages, also suggests periods when the exposure of the Agulhas Bank likely influenced interactions between the Agulhas and Benguela current systems, enhancing productivity in the southern Cape Basin. Overall, these records highlight a coupled system in which sea level, frontal position, and ocean current dynamics jointly control nutrient delivery and ecosystem structure. Siliceous microfossil evidence of changes in circulation and primary productivity in the Cape Basin significantly refines the timing and mechanisms of Southern Ocean reorganization during the MPT.