We present sea surface and upper thermocline temperature records (60-100 year temporal resolution) spanning marine isotope stage 3 (similar to 24-62 ka B. P.) from International Marine Global Change Study core MD01-2378 (121 degrees 47.27'E and 13 degrees 04.95'S; 1783 m water depth) located in the outflow area of the Indonesian Throughflow within the Timor Sea. Stable isotopes and Mg/Ca of the near-surface-dwelling planktonic foraminifer Globigerinoides ruber (white) and the upper thermocline-dwelling Pulleniatina obliquiloculata reveal rapid changes in the thermal structure of the upper ocean during Heinrich events. Thermocline warming and increased delta O-18(seawater) (P. obliquiloculata record) during Heinrich events 3, 4, and 5 reflect weakening of the relatively cool and fresh thermocline flow and reduced export of less saline water from the North Pacific and Indonesian Seas to the tropical Indian Ocean. Three main factors influenced Indonesian Throughflow variability during marine isotope stage 3: (1) global slowdown in thermohaline circulation during Heinrich events triggered by Northern Hemisphere cooling, (2) increased freshwater export from the Java Sea into the Indonesian Throughflow controlled by rising sea level from similar to 60 to 47 ka, and (3) insolation-related changes in the Australasian monsoon with associated migration of hydrological fronts between Indian Ocean- and Indonesian Throughflow-derived water masses at similar to 46-40 ka.