The Indonesian Throughflow (ITF) inflow through the Sulawesi, Maluku, and Halmahera Seas and the ITF outflow into the eastern tropical Indian Ocean, based on reanalysis and model data, are used to investigate the interannual to decadal response of the ITF vertical profile to Indo‐Pacific forcing. The thermocline (upper 300 m) inflow, driven by the North Pacific Ocean, negatively responds to El Niño‐Southern Oscillation (ENSO) with almost no lag; while the thermocline outflow lags by 5–7 months. The sub‐thermocline (300–760 m) inflow, which is influenced by both the North and South Pacific, positively responds to ENSO and Interdecadal Pacific Oscillation (IPO) indices with 13 months lag and displays a long‐term trend tracking the IPO index. Influenced by eastern Indian Ocean variations, the sub‐thermocline outflow positively correlates with the ENSO and IPO indices with about 7–9 months lag, a shorter lag time than the inflow.
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