In the Southern Hemisphere, changes in the hydrodynamics and biogeochemistry in the upper water column play an essential role in global ocean circulation and climate. Expansions or contractions of the Southern Ocean and changes in the meridional variability of the Subtropical Front (STF) can influence global ocean circulation by moderating the magnitude of water exchange at the Indian-Atlantic Ocean Gateway, so-called Agulhas Leakage. Here we present new biomarker records of upper water column temperature (U_37^k' and TEX86), primary productivity (chlorins and alkenones), and sea surface salinity (δDalkenone) from marine sediments at IODP Site U1475 on the Agulhas Plateau, near the STF and within the Agulhas retroflection pathway. We use these multiproxy time-series records from 3.6 to 1.9 and 1.4 to 0.3 Ma to examine implied changes in the upper oceanographic conditions during the Plio-Pleistocene and early to middle Pleistocene transitions. Our reconstructions suggest that during the Plio-Pleistocene (3.6 – 1.9 Ma), the STF reached its most northward position during Marine Isotope Stage (MIS) M2. This northward migration not only affected the upper water column hydrology and biogeochemistry at the Agulhas Plateau but significantly reduced Agulhas leakage during the period between 3.3 - 3.15 Ma. Combined with prior evidence, upper water temperatures, sea surface salinity (SSS), and changes in primary productivity at the Agulhas Plateau suggest the Agulhas leakage was reestablished after 2.7 Ma.Our multiproxy approach across the mid-Pleistocene transition (MPT, ca. 1.2–0.8 Ma) suggests that in the Southwestern Indian Ocean, the STF was further south from the Agulhas Plateau during the mid-Pleistocene Interim State (MPIS, 0.9 - 0.47 Ma) and reached its northernmost position during MIS 34-24 and MIS 10. We also present evidence that only the most extreme northward migrations of the STF are associated with reduced Agulhas leakage. We suggest shifting westerly winds may exert a stronger influence over Agulhas Leakage variability than latitudinal migrations of the STF.