The tectonically active Makran Subduction Zone (MSZ) overlooks Oman’s northern coast, where the Eurasian and Arabian Plates meet in the Sea of Oman. There have been significant tsunamis and earthquakes caused by the MSZ in the past. A recent non-tsunami event in northern Oman led to hydrodynamic and morphological alterations, as well as changes in coastal stability, which were explored in this study. An integrated module for hydrodynamics, waves, and sediment flow is assigned to carry out process-based numerical modeling. To manage a two-dimensional hydrodynamic flow system, CMS-Flow and CMS-Wave steering modules were employed. Tidal currents exhibit spatial variability due to bathymetric and geographic complexity. This, combined with sediment transport channels that follow tide-related asymmetry patterns, results in an apparent asymmetry between ebb and flood flows. The annual morphological change in the region around the port of Sohar is not affected by waves created by northwesterly high winds, despite the fact that these waves have the capacity to redistribute sediments. As shoals are propelled by waves/winds in the same direction, their currents are not as predictable as those generated by waves/winds. This study’s computational sediment transport model shows that flood-driven transport happens mostly on the east side of the port of Sohar. There has been very little accumulation of intertidal sand shoals in the port, as shown by the model; this suggests that sediment filling has progressed very slowly, which could lead to navigational hazards over time. While flood control measures have been necessary for Sohar’s coastal area, they will be unnecessary shortly as the port’s eastern section is expected to shift from flood to ebb dominance and act as a source of sediment rather than sink.