Vertical mixing in the Indonesian Seas has been considered to be responsible for the apparent freshness of the throughflow when 'it enters the Indian Down. A three-dimensional primitive equation numerical model of the Indonesian Seas forced with a prescribed throughflow, transport consisting of North Pacific waters, is used to determine local dynamic processes which may modify the characteristics of the throughflow properties. The lack of long-term current measurements in the Indonesian Seas presents some difficulties in determining the certainty of the derived velocity fields. As an alternative, the model temperature and salinity fields are compared to observed hydrographic data which has a relatively better coverage throughout the Indonesian Seas. A 15 Sv net transport through the Indonesian Seas is suggested based on the model’s more realistic reproduction of the hydrographic structure compared to a throughflow with a smaller magnitude. A pure North Pacific source for the throughflow is also not capable of producing the salinity structure in the Banda Sea as suggested by previous studies and the required amount of salt to fit the model salinity structure with observations in the Banda Sea is estimated to be 3.3x10‘3 kg. Most of the throughflow transport occurs in western boundary flows and is largely topographically controlled. The separation of an upper and lower layer circulation pattern is controlled by the depth of the sill in Makassar Strait. Vertical excursions in the vicinity of this sill seen level of the in model results coincide upper salinity maximum with regions where are found. Seasonal large horizontal gradients at the upwelling and longer residence times due to weaker flows in the Banda Sea results in a more effective mixing of the already weakened salinity structure of the waters from Makassar Strait/Flores Sea. Net heat and freshwater flux estimates also reveal significant departures at 200 up to 100 m between the Pacific inflow and Indian outflow, suggesting the considerable redistribution of heat and salt in the Indonesian Seas.