This study describes typical mass transports in spring, summer, autumn and winter in Tokyo Bay by using a non-hydrostatic model, MEL3D. Some typical salinity and water temperature distributions in each season obtained from field observation were used in the numerical computation. Furthermore, spatial distributions of wind over Tokyo Bay evaluated using nine meteorological observation stations were applied in the computation as boundary conditions. To investigate mass transport, neutral particle tracking simulations were carried out by putting particles along near the coastal line by about 4km. As the results, especially in summer, it was demonstrated that the characteristic of the neutral particle transport in Tokyo Bay is strongly affected by the vertical current of circulation around the western coast in the head of Tokyo Bay.