Accurate reconstructions of ocean circulation over geologic time provide climate models with critical information used for configuration and validation. These reconstructions rely largely on paleoceanographic datasets, however certain regions remain unexplored and create uncertainty in model predictions. This study focuses on constraining the behavior of two specific ocean currents in the Southern Hemisphere in the Plio-Pleistocene (3.5 to 1.5 Ma), namely the Indonesian Throughflow (ITF) and the Antarctic Circumpolar Current (ACC). The ITF travels through the Indonesian Gateway and transports warm equatorial Pacific waters into the Indian Ocean, ultimately driving the strength and intensity of the southward flowing Leeuwin Current along the western coast of Australia. It therefore influences the amount of warm water reaching high-latitude current systems such as the ACC. Despite its importance to both low and high latitude climate, significant debate still exists on the timing of Plio-Pleistocene oceanographic changes around the ITF. Furthermore, outstanding questions remain on the influence of the ITF on nearby Australian continental paleoclimate. The other focus of this study, the ACC, is the strongest and fastest moving current on the planet that mixes and redistributes water between all major ocean basins. Furthermore, the ACC is the primary connection between Antarctica and the rest of the globe. While fundamentally important to atmosphere-ocean-cryosphere dynamics in the Southern Hemisphere, the ACC remains poorly constrained through geologic time due to an overall lack of long, continuous sedimentary records under its influence. Here we use a suite of different organic geochemical biomarker proxies preserved in marine sediments to reconstruct the behavior of the ITF and the ACC over geologic time. We also examine the relationship between both currents and Australian continental paleoclimate. Finally, we thoroughly investigate the applicability and limitations of different biomarker proxies in reconstructing paleoenvironmental conditions. Results fill several critical gaps in our understanding of Southern Hemisphere paleoclimate, contribute to ongoing collaborative work with the International Ocean Discovery Program (IODP), and provide insight into complex organic geochemical biomarker dynamics in marine sediments.