Makassar Strait conveys the main Indonesian Throughflow (ITF) pathway, as part of the global thermohaline circulation transferring heat and freshwater fluxes from the Pacific Ocean to the Indian Ocean. Dynamics and variability of the ITF and the monsoon winds system influence significantly marine ecosystem in the Indonesian Seas. The study aims to analyze sea surface circulation patterns and particle trajectories in the Makassar Strait by developing a simulation of the CROCO’s 1/36º regional general circulation model between 2017-2018. The results revealed the dynamics of near-surface layer (0 – 50 m depth) varied seasonally. The magnitude of surface current was about 0.6 m/s during the peak of northwest monsoon (NWM) flowing northward and reverse southward during the peak of southeast monsoon (SEM). The magnitude of the current intensified up to 1 m/s in the subsurface at Labani Channel and persistent flows to the southward. The thermocline transport volume was maximum during SEM with average transport about -11.00 (±1.54) Sv. The analysis shows that the particles near Balikpapan coast spreaded slowly to the north, then rotating at the center of the strait and spreaded according to the NWM and SEM.