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Abstract The Makassar Strait, the main passageway of the Indonesian Throughflow (ITF), is an important component of Indo‐Pacific climate through its inter‐basin redistribution of heat and freshwater. Observational studies suggest that wind‐driven freshwater advection from the marginal seas into the Makassar Strait modulates the strait's surface transport. However, direct observations are too short (<15 years) to resolve variability on decadal timescales. Here we use a series of global ocean simulations to assess the advected freshwater contributions to ITF transport across a range of timescales. The simulated seasonal and interannual freshwater dynamics are consistent with previous studies. On decadal timescales, we find that wind‐driven advection of South China Sea (SCS) waters into the Makassar Strait modulates upper‐ocean ITF transport. Atmospheric circulation changes associated with Pacific decadal variability appear to drive this mechanism via Pacific lower‐latitude western boundary current interactions that affect the SCS circulation.