A two-dimensional dynamical model is established to simulate current circulation and sediment transport induced by storm surges in a schematic harbor. The model accounts for both settling and resuspension processes of cohesive fine sediments in a salty water environment. The numerical results demonstrate that the current follows wind albeit with a time lag, and so does sediment concentration. The time lag between current and wind is of the order of interval needed for wind to transfer momentum to the whole water body. Whereas, the retarded dynamic balance of sediment entrainment and settling fluxes is responsible for the time lag between sediment concentration and current. When a tropical cyclone, or conventionally so-called typhoon in the Pacific area, is passing through the harbor, the higher sediment concentration inside the harbor is found to the right of the path rather than to the left of it. Bed deformation is found to be substantially influenced by typhoon tracks relative to the harbor. For a harbor facing east, a northward typhoon results in erosion and the southward or westward one causes deposition. Both erosion and deposition occur along the coast with little bedform variations near the harbor center.