Abstract Multidecadal variability of the Indonesian Throughflow (ITF) is crucial for the Indo-Pacific and global climate due to significant interbasin exchanges of heat and freshwater. Previous studies suggest that both wind and buoyancy forcing may drive ITF variability, but the role of precipitation and salinity effect in the variability of ITF on multidecadal time scales remains largely unexplored. Here, we investigate the multidecadal changes and long-term trend of the ITF transport during the past six decades, with a focus on the role of precipitation and salinity effect. The diverse datasets consistently indicate a substantial upward trend in the halosteric component of geostrophic transport of ITF in the outflow region at 114°E during the six decades. We find that the meridional differences of the salinity trend in the outflow region explain the increasing trend of the halosteric component of ITF transport. On a larger scale, the tropical western Pacific Ocean and Indonesian seas have experienced significant freshening, which has strengthened the Indo-Pacific pressure gradient and thus enhanced the ITF. In contrast, the equatorial trade wind in the western Pacific Ocean has weakened over recent decades, implying that changes in wind forcing have contributed to weakening the ITF. The combined effect of strengthened halosteric and weakened thermosteric components has resulted in a weak strengthening for the total ITF with large uncertainties. Although both the thermosteric and halosteric components are associated with natural climate modes, our results suggest that the importance of salinity effect is likely increasing given the enhanced water cycle under global warming.