THE physical structure of the Pacific and Indian oceans is substantially affected by the inter-ocean transport of excess fresh water from the North Pacific Ocean through the Indonesian seas(1,2). The efficiency of this transport is an important regulator of the meridional overturning of these oceans(1,2), and hence perhaps of the global thermohaline circulation(3); in addition the seepage of warm water out of the Pacific affects the volume of the western Pacific warm pool, and thus may influence El Nino events(24). But the sources, pathways and physical properties of the Indonesian throughflow are not well enough characterized to allow its influence on ocean circulation and the climate system to be quantified. Here we report salinity, temperature and chemical-tracer data from the Indonesian seas which show that the throughflow is dominated by two components : one of low-salinity, well ventilated North Pacific water through the upper thermocline of the Makassar Strait, and the other of more saline South Pacific water through the lower thermocline of the eastern Indonesian seas. Seasonal (monosonal) variations in the ratio of these components, perhaps modulated by El Nino conditions, imply the existence of potentially important variable feedbacks to the ocean circulation and climate system.