The Makassar Strait, located between Kalimantan (Indonesian Borneo) and Sulawesi, plays a crucial role in Indonesian Throughflow (ITF) and regional oceanography. It connects the Pacific and Indian Oceans and significantly influences water exchange between the two basins. While ITF is recognized as a primary driver of Makassar Strait dynamics, salinity variation also contributes to its seasonal variability. Here, we analyze the effects of salinity on the seasonal variability of the Makassar Strait throughflow using 25 years of ocean reanalysis data and in situ observations. Our results show that the inflow transport in the Makassar Strait is negatively correlated with sea surface salinity, suggesting an inverse relationship between salinity and transport strength. Moreover, salinity changes impact the pathway of the ITF through the Makassar Strait, influencing the surface circulation within the strait. Furthermore, we suggest that salinity effects could play a pivotal role in interannual-to-decadal variability of the Makassar Strait throughflow, but further investigation is required to verify these connections.