A three-dimensional hydrostatic numerical simulation on tsunami-induced topography changes near a harbor is carried out, and sediment transport processes on a significant local deposition near the center of the harbor caused by a tsunami, which was observed in an early experimental study, are investigated. This local deposition has not been well predicted by a vertically averaged hydrodynamic model. The results show that velocities, water levels and topography changes in the harbor predicted in this study agree with the experimental data. The local deposition has relations with a vortex generated in the harbor when the tsunami attacks the harbor. At areas near the vortex center, a secondary flow of the first kind develops, and it plays the role of transporting suspended sediment to the vortex center, located near the center of the harbor, and causes the local deposition there. In order to predict deposition areas with high accuracy, the secondary flow effects should be incorporated in prediction methods of tsunami-induced topography change.