Abstract The distribution and configuration of water properties are described along five hydrographic sections that cross the Indonesian Throughflow at two longitudes not far from the outflow straits. Properties are further analyzed through the use of concentration anomalies along neutral surfaces. The analysis confirms the two core structure of the Indonesian Throughflow, which has distinct thermocline and intermediate water components. The latter occupies a larger area than the former on all five sections. Westward increase in the salinity of the South Equatorial Current, which carries the Indonesian Throughflow, implies that lateral entrainment and recirculation of saltier thermocline waters of Indian Ocean origin must occur in the region. Relatively salty North Indian Ocean water is advected eastward south of Java within and below the South Java Current. While the upper portion of this flow appears ‘blocked’ at Lombok Strait by the Throughflow, the deeper portions penetrate further east below the Lombok sill depth (350 m). A rather complex intermediate water circulation in the Southeast Indian Ocean is found involving the recirculation of waters of Indian Ocean origin between a set of zonal currents crossed by the sections. An intermediate water countercurrent (counter to the sense of the Sverdrup flow above it) is described, flowing eastwards between the edge of the subtropical gyre and the Indonesian Throughflow.