Abstract Climate models project a weakening of the Indonesian Throughflow (ITF) under future warming, but how this manifests in the vertical flow structure of individual passageways and its implications for inter‐basin freshwater transport remains uncertain. Using state‐of‐the‐art climate model simulations, we explore future volume and freshwater transport changes across all three inflow pathways. We find that Pacific wind stress curl changes induce a southward migration of equatorial currents that reduce surface transport through the Halmahera Sea. The projected weakening of the Atlantic Meridional Overturning Circulation generates Kelvin waves that propagate into the ITF region and weaken thermocline and intermediate flow through Makassar Strait and Maluku Sea. Despite decreasing volume transport, ITF freshwater transport is projected to increase due to enhanced regional precipitation. Our results highlight the remote and regional processes that will modulate ITF circulation under future warming.

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