The dynamics of marine microplastics in Tokyo Bay, which have been a concern for marine organisms, were analyzed using a mathematical model. In this paper, three equations (dissolved form, small particles with sedimentation rate, and large particles adsorbed form) are constructed for microplastics loaded from rivers in Tokyo Bay, and the number density analysis method is developed by considering adsorption/desorption, mineralization, and sedimentation effects among them. The distribution coefficients of microplastics were parameterized with reference to dioxins. When the distribution coefficient was 20 times larger than that of dioxins, the number density analysis of microplastics in Tokyo Bay showed high reproducibility compared to the measured data. The analysis results show that the discharge of microplastics into the bay is about 30%.