The Indonesian Throughflow (ITF) is the only low-latitude conduit for exchange of surface and thermocline waters between the Indian and Pacific Oceans; 80% of the ITF waters pass through the Makassar Strait. The flux of heat and salt through the strait is, in part, a function of the density difference between its southern and northern ends. Here the Mg/Ca and stable oxygen isotope compositions of the planktonic foraminifer Globigerinoides ruber sampled from two sediment cores collected at the northern and southern ends of the Makassar Strait are used to reconstruct surface-water temperature (SST), sea-surface salinity (SSS), and seawater density variability over the past 2000 yr. Maximum SST and SSS occurred at both sites between 850 and 700 yr ago, coinciding with the Medieval Solar Maximum and Medieval Warm Period (ca. 1000–700 yr ago). SST and SSS declined at both locations after 700 yr ago and reached minimum values during the Little Ice Age, between 300 and 100 yr ago. However, the magnitude of SST and SSS change over the past 2000 yr was distinctly different between the two sites, especially during the period between 2000 and 900 yr ago. This led to changes in the south to north density gradient within the Makassar Strait. Specifically, the time interval from ca. 2000 to 800 yr ago was marked predominantly by higher densities at the northern end relative to the southern end of the strait, suggesting reduced heat flux from the Pacific to the Indian Ocean. This is consistent with previous work showing that this time interval was also marked by frequent El Niño conditions. Conversely, the period from ca. 800 to 300 yr ago, including the LIA, was marked by frequent periods when surface density was higher at the southern end of the strait, indicative of enhanced heat flux to the Indian Ocean.