We measured oxygen isotopes and Mg/Ca ratios in the surface-dwelling planktonic foraminifer Globigerinoides ruber (white s.s.) and the thermocline dweller Pulleniatina obliquiloculata to investigate upper ocean spatial variability in the Indo-Pacific Warm Pool (IPWP). We focused on three critical time intervals: the Last Glacial Maximum (LGM; 18-21.5 ka), the early Holocene (8-9 ka), and the late Holocene (0-2 ka). Our records from 24 stations in the South China Sea, Timor Sea, Indonesian seas, and western Pacific indicate overall dry and cool conditions in the IPWP during the LGM with a low thermal gradient between surface and thermocline waters. During the early Holocene, sea surface temperatures increased by similar to 3 degrees C over the entire region, indicating intensification of the IPWP. However, in the eastern Indian Ocean (Timor Sea), the thermocline gradually shoaled from the LGM to early Holocene, reflecting intensification of the subsurface Indonesian Throughflow (ITF). Increased surface salinity in the South China Sea during the Holocene appears related to northward displacement of the monsoonal rain belt over the Asian continent together with enhanced influx of saltier Pacific surface water through the Luzon Strait and freshwater export through the Java Sea. Opening of the freshwater portal through the Java Sea in the early Holocene led to a change in the vertical structure of the ITF from surface- to thermocline-dominated flow and to substantial freshening of Timor Sea thermocline waters.