This dataset explores the variability in glacial-interglacial surface hydrography in the western Indian Ocean across the middle to late Pleistocene. Here, we provide 1kyr resolution Mg/Ca-based sea surface temperatures and surface oxygen isotope ratios of seawater (ice volume corrected) as proxy for surface palaeo-salinity from surface dwelling foraminifera Globigerinoides ruber from International Ocean Discovery Program core site U1476 located in the Mozambique Channel, which we use in combination with other records to create Indian Ocean sea surface salinity and sea surface temperature stacks. The data show increases in sea surface temperature and salinity during glaciation, with maximum temperature and salinity occurring at glacial maxima, prior to global deglaciations as indicated by benthic oxygen isotopes, a proxy for global ice volume. Lead-lag analyses were conducted using cross-spectral analysis between sea surface temperatures, salinity, and benthic oxygen isotopes. In parallel, sea-to-land pixel ratios from the ANICE-SELEN model across the Indonesian Archipelago show changes in land surfacing in the Indonesian archipelago due to globally sinking sea levels. The increase in surface temperature and salinification at U1476 occurs at the same time as major land surfacing in the Indonesian Archipelago suggesting a mechanistical link between land surfacing due to global sea level lowering, and changes in Indian Ocean surface hydrography that appears to be a resulting reduction in the considerably fresher Indonesian throughflow entering the Indian Ocean.