Helium isotope measurements from the Indonesian Seas, and from the Java-Australia Dynamic Experiment cruises define mantle 3He sources and deep water spreading patterns. 3He sources in the Sulawesi Sea and in the Makassar Strait are found, but these are prevented from spreading into the Banda Sea and the Indian Ocean by blocking sills. A major mantle source is identified below 2000 m in the Flores Sea. The 3He distribution suggests that the Banda Sea water migrates westward along the floor of the Flores Sea, upwells and then advects the high 3He Flores signal. A tongue of higher-than-ambient 3He on the Indian Ocean side of the Flores chain indicates a deep outflow of the Flores and the Banda Sea water into the Indian Ocean near 1300 m.¿ 1997 American Geophysical Union