As the only low-latitude connection between ocean basins, the Indonesian Throughflow allows the direct transmission of heat and salinity between the Pacific and Indian Oceans. Despite its potential importance, the role of the Indonesian Throughflow in global ocean circulation and regional climate is still not clear due to sparse measurements and the relative difficulty of modeling the region. The Mg/Ca and [delta]¹⁸0 of calcite of the calcitic planktic foraminifera Globigerinoides ruber (G. ruber) were used to estimate the sea surface temperature and [delta]¹⁸0 of water, an indicator of hydrologic conditions, over the past 20,000 years. I also attempted to estimate thermocline structure using the foraminifera, Pulleniatina obliquiloculata, but the Mg/Ca and [delta]¹⁸0 of calcite data yield conflicting interpretations, indicating further work on this proxy is required. The G. ruber Mg/Ca results suggest that the sea surface temperature of the outflow passages was influenced by high latitude Southern Hemisphere temperature. This connection is likely via intermediate waters that upwell in the Banda Sea. At approximately 10,000 years before present, there was a warming in the Makassar Strait. This local warming was coincident with the flooding of the Sunda Shelf, which opened a connection between the South China Sea and the Indonesian Throughflow. Regional [delta]¹⁸0 of seawater reconstructions show that during the last glacial maximum the [delta]¹⁸0 of seawater pattern was very similar to modern, but there were relatively enriched values over the equatorial IndoPacific during high latitude Northern Hemisphere cold events (Heinrich Stadial 1 and the Younger Dryas). From these results we postulate that the mean position of the Intertropical Convergence Zone was approximately the same as modern at the last glacial maximum and was likely displaced to the south during the Younger Dryas and Heinrich Stadial 1, suggesting the Intertropical Convergence Zone primarily responds to changes in the interhemispheric temperature gradient. These results shed light on the primary controls of the temperature and hydrology of Indonesian Throughflow region.