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 2000m 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 1300m.