Abstract : The magnitude and variations of the Pacific to Indian Ocean throughflow within the Indonesian Seas are considered to be key elements in the thermohaline balance of the Indian and Pacific Oceans, and perhaps to the global climate system. Local variability of the Indonesian Seas may influence ENSO by governing the transfer of the warm tropical water between the Pacific and Indian Oceans. Furthermore, advective and tidal induced mixing may influence the SST and sea-air coupling, with feedback on ENSO. The Arlindo Project is a joint oceanographic research endeavor of Indonesia and the United States. Arlindo s goal is to resolve the circulation and water mass stratification within the Indonesian Seas in order to formulate a thorough description of the source, spreading patterns, inter-ocean transport and dominant mixing processes within the Indonesian Seas.