The surface waters around Southern Africa (SA) are a confluence of the Benguela Upwelling System (BUS), the Agulhas System, and the Antarctic Circumpolar frontal system. The Subtropical Front (STF) is largely considered the boundary between the Antarctic Circumpolar frontal system and the Agulhas System; northward shifts of the STF are thought to limit the intensity of Agulhas Leakage (AL). Here, we present a new leaf wax hydroclimate record from ODP 1084, in the BUS. This and regional proxy records reveal that substantial changes in the isotopic signature of precipitation over SA coincide with significant shifts in the position of the STF and intensity of AL across the Mid-Pleistocene Transition. Archaeological sites in SA suggest occupation by early humans during the Mid-Pleistocene - changes in water availability and rainfall seasonality may have been a source of stress for these populations. Given the ongoing impacts of climate change on water resources in SA, awareness of the relationship between rainfall and STF shifts could not only provide insight into past water availability, but also aid regional adaptation efforts.