Oil spills (OS) in waters can have major consequences for the ecosystem and adjacent natural resources. Therefore, recognizing the OS spread pattern is crucial for supporting decision-making in disaster management. On 31 March 2018, an OS occurred in Balikpapan Bay, Indonesia, due to a ship’s anchor rupturing a seafloor crude oil petroleum pipe. The purpose of this study is to investigate the propagation of crude OS using coupled three-dimensional (3D) model from DHI MIKE software and remote sensing data from Sentinel-1 SAR (Synthetic Aperture Radar). MIKE3 FM predicts and simulates the 3D sea circulation, while MIKE OS models the path of oil’s fate concentration. The OS model could identify the temporal and spatial distribution of OS concentration in subsurface layers. To validate the model, in situ observations were made of oil stranded on the shore. On 1 April 2018, at 21:50 UTC, Sentinel-1 SAR detected an OS on the sea surface covering 203.40 km². The OS model measures 137.52 km². Both methods resulted in a synergistic OS exposure of 314.23 km². Wind dominantly influenced the OS propagation on the sea surface, as detected by the SAR image, while tidal currents primarily affected the oil movement within the subsurface simulated by the OS model. Thus, the two approaches underscored the importance of synergizing the DHI MIKE model with remote sensing data to comprehensively understand OS distribution in semi-enclosed waters like Balikpapan Bay detected by SAR.