Minamata Bay which suffered from a major disaster called "Minamata Disease" has already remediated from 1977 to 1990 by carried out highly mercury (Hg) contaminated sediment and reclaimed it in the bay area. Furthermore, many studies reported that the mercury has reached Yatsushiro Sea, the outer part of Minamata Bay. It can be assumed that the sediment transport still occurs from remaining Hg concentration even after the remediation project. In order to investigate it, we try to simulate the transport of sediment contaminated by Hg from Minamata Bay to the Yatsushiro Sea with different coastal morphology on before and after the reclamation projects.Sediment transport and tidal flow with rectangular variable grid both before and after reclamation conditions around the Yatsushiro Sea and Minamata Bay are simulated by DELFT3D. The initial bottom sediment thickness of 1m is set in the only inner side of the bay and six months simulation results for both before and after reclamation area are compared. The change of hydrodynamic condition inside Minamata Bay due to the remediation project gives a slight change in sediment transport pattern. It is estimated that after the reclamation, the sediment transport moves slower than before it due to the change of its magnitude of velocity above the seabed. As an important result, it is clarified that a change of the amount of bottom sediment which can be re-suspended in Minamata Bay caused by the topographical change can also affect the pattern. Also, this result suggests that the southern part of Yatsushiro Sea can be influenced by sediment contaminated by higher Hg included before the reclamation project.