High sea surface temperatures in the western Pacific warm pool fuel atmospheric convection and influence tropical climate. This region also hosts the Indonesian throughflow, the network of currents through which surface and thermocline waters are transported from the western equatorial Pacific Ocean into the Indian Ocean. Here we show, using records of the Δ18 O and Mg/Ca of planktonic foraminifera from eight sediment cores, that from about 10,000 to 7,000 years ago, sea surface temperatures in the western sector of the western Pacific warm pool were about 0.5 °C higher than during pre-industrial times. We also find that about 9,500 years ago, when the South China and Indonesian seas were connected by rising sea level, surface waters in the Makassar Strait became relatively fresher. We suggest that the permanent reduction of surface salinity initiated the enhanced flow at lower, thermocline depths seen in the modern Indonesian throughflow. However, the uniformly warm sea surface temperatures found upstream and downstream of the Indonesian throughflow indicate that the early Holocene warmth in this region was not directly related to reduced heat transport by the throughflow that may have resulted from surface freshening of the Makassar Strait. Instead, we propose that the elevated temperatures were the result of a westward shift or expansion of the boundaries of the western Pacific warm pool. © 2010 Macmillan Publishers Limited. All rights reserved.