Indian Ocean surface circulation is an important part of the global ocean conveyor belt, and is connected via two important gateways including the Indonesian Throughflow, and the Agulhas Leakage. Changes in the surface hydrography of the Indian Ocean may therefore impact on the global overturning circulation. Using planktonic foraminifera-based reconstructions of Indian Ocean surface salinity and temperature, we find that Indian Ocean surface water became saliter during glacial intensification. Here we present bathymetrical change data for the Indonesian Archipelago which shows that the Indonesian Throughflow was likely impacted due to changes in global mean sea level and possibly drove the changes in salinity during a glacial cycle.