The relationship of Indonesian throughflow (ITF) transport to the El Niño Southern Oscillation (ENSO) is investigated. Seasonal anomalies of ITF transport are found to be forced by anomalous local, alongshore (South Java) wind as well as by anomalous winds in the equatorial Pacific and Indian Oceans. Ocean stratification, set up by surface freshwater fluxes and the ITF, partitions the anomalous forcing onto two separate layers in the ITF region, a near surface layer (approximately the upper 100 m) and a thermocline layer (approximately 100–500 m). Interannual anomalies in alongshore South Java winds and equatorial Indian Ocean winds cause changes in upper ocean ITF transport, while divergent winds over the equatorial Pacific and Indian Oceans control thermocline layer transport anomalies. Interannual periods when the total depth-integrated transport is most weak occur when there are anomalous westerlies in the equatorial Pacific, anomalous easterlies in the equatorial Indian Ocean (resulting in reduced thermocline level transport), and anomalous westerlies along the coast of southern Java (causing reduced upper ocean transport). Such conditions are found when there are cold sea surface temperature anomalies in the Indonesian Seas as well as the equatorial Indian Ocean, and thus are not strictly related to ENSO variability. Interannual variations in the ITF therefore are controlled by interannual variability associated with ENSO as well as by interannual variability in the Indian Ocean.