The region on either side of the equator between the islands of the Indonesian archipelago. This has the most complicated topography of any of the regional seas of the world, consisting of a series of deep basins with limited interconnections, each characterized by its own type of bottom water of great age. The basins comprising this include the Banda, Sulawesi (formerly Celebes), Molucca, Halmahera, Serman, Sulu, Flores, Java and Sawu Seas, with the Banda being the largest and deepest.

The net transport is believed to be westward at all times, from the Pacific to the Indian Ocean, with a maximum in August (estimated at 12-20 Sv) and a minimum in February (estimated at 2-5 Sv). It takes the form of a western boundary current that is strongest along Mindanao and and Kalimantan. The transport also occurs mainly in the upper layers with little transport below 500 m and about 75% above 150 m. Most of the high salinity input occurs across the sill between the Pacific and the Sulawesi Sea, while most of the low salinity output is through various narrow passages between the south Indonesian islands, with both input and output occurring over the entire water depth over the sills.

The freshening of the throughput occurs due to both high freshwater input from seasonal precipitation and to strong turbulent mixing that effects water mass conversion in the upper 1000 m of the water column, with the turbulence probably due to locally strong tidal currents. This mixing process imparts a unique character to the Australasian Mediterranean in that the salinity field in the upper 1000 m is nearly homogeneous while the temperature field is still stratified. This occurs because even though both temperature and salinity are strongly mixed the intense solar heating in the region serves to maintain the temperature stratification.