The properties of the waters that move from the Pacific to the Indian Ocean via passages in the Indonesian archipelago are observed to vary with along-flow-path distance. We study an ocean model of the Indonesian Seas with reference to the observed water property distributions and diagnose the mechanisms and magnitude of the water mass transformations using a thermodynamical methodology. This model includes a key parameterization of mixing due to baroclinic tidal dissipation and simulates realistic water property distributions in all of the seas within the archipelago. A combination of air–sea forcing and mixing is found to significantly change the character of the Indonesian Throughflow (ITF). Around 6 Sv (approximately 1/3 the model net I...