The Makassar Strait (MS) is directly connected to the Sulawesi Sea in the north and the Java Sea and the Flores Sea in the south and is the main route of Indonesia Throughflow(ITF). Hence Stratification of water mass in the MS is influenced by the dynamics of these waters. This study aims to describe seasonal variations of the mixed layer depth and the thermocline thickness, identify ITF water masses, and the occurrence of coastal upwelling in the southern part of the MS. The results show that the North Pacific water origin of North Pacific Subtropical Water (NPSW) and North Pacific Intermediate Water (NPIW) are dominant, with a maximum salinity characteristic of 34.6-34.7 psu in the thermocline layer and a minimum salinity of 34.5 psu in the intermediate layer. However, near-surface fresh Java Seawater appears to be dominant during the northwest monsoon (NWM-DJF) period. Seasonal variation of the mixed layer depth is much deeper (93m) and vertical gradient of temperature and salinity are much stronger due to the presence of fresh Java Sea water advected by the eastward Java Monsoon Current. However, during the southeast monsoon (SEM-JJA) period the mixed layer depth is much shallower and the thermocline layer is much thicker (198 m), Associated with much stronger ITF and upwelled colder water from the upwelling area. The coastal upwelling event during the SEM period in the study are is characterized by an increase of isotherm of 25 °C, isohaline of 34.0 psu, and isopycnal of 22.0 kg/m3 from about 75 m depth to the sea surface layer.