Using an ocean general circulation model, we find that the vertical profile of the Indonesian Throughflow (ITF) transport is important in regulating the stratification and surface heat fluxes of the Indian Ocean. With the same total ITF transport, a thermocline-intensified ITF, relative to a surface-intensified ITF, not only cools the surface layer of the Indian Ocean while warming the Indian Ocean below the thermocline, but also induces negative temperature anomalies at the sea surface throughout the Indian basin. As a consequence of this surface effect the net heat gain of the Indian Ocean is increased. The results suggest that it is necessary to properly represent the vertical profile of ITF transport within ocean and climate numerical models.
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