<p>The Malacca Strait permits salt exchange between the western Pacific Ocean and the Andaman Sea in the northern Indian Ocean. Here, we show a joint inter-basin mechanism that modulates the freshwater exchange through the Malacca Strait using reanalysis and remote sensing datasets. The salinity variation within the Malacca Strait and the southern Andaman Sea is related to both the volume transport and the properties of the source water to the Malacca Strait that all experience interannual variability due to the climate modes from the Indian and Pacific Oceans. On interannual time scales, the Indian Ocean Dipole (IOD)-related anomalous wind pattern prevails in the boreal summer and autumn, acting to modulate the seasonal volume transport of the Malacca Strait such that there is a strengthened (weakened) transport in boreal summer-autumn during positive (negative) IOD events. An atmospheric moisture budget analysis shows that the moisture divergence term governs the source water through the Malacca Strait, with a saltier (fresher) transport during El Niño (La Niña). Taken together, the joint modulation reveals separate contributions from the Pacific and Indian Oceans through interbasin dynamics in governing salinity transport on interannual time scales, suggesting substantial impacts on water properties and exchange through the Malacca Strait.</p>