On 31 March 2018, an oil spill accident polluted Balikpapan Bay. A failure occurred in a pipeline running from Penajam to Balikpapan Oil Refinery, East Kalimantan, Indonesia. Leaking pipeline caused the total estimated volume of leaked oil to approximate 44,000 Barrels of crude oil. MoTuM was used to simulate the dispersion of oil in the area. The modeling results indicate that a strong dynamic tidal current in the Bay controls the oil’s movement. The MoTuM software is suitable for spill combating, contingency plans, and backtracking. MoTuM is developed in Windows System, which integrates 3D Non-Orthogonal Boundary Fitted Ocean Hydrodynamics Model, Trajectory, Fates, Stochastic, Backtracking in Geographic Information System. This paper presents a further study of the effect of non-linear waves on the dispersion of oil in the Bay. The simulation results were validated by comparing the model with a satellite image. The agreement between the result of simulation and satellite image is excellent and shows that the non-linear wave is an essential factor for oil spill dispersion.