Object of this study is to predict distribution of deposited dioxins in the bottom of Tokyo Bay by means of a 3-dimensional flow model (a Hybrid Box Model) linked with a diffusion model. To improve accuracy of the analyses of dioxins concentration, the absorption-desorption processes, aggregation-disaggregation processes, sinking of suspended substances and other factors are taken into account. On the basis of the load fluxes from rivers, the distribution of concentration (separately for dissolved dioxin and small and large particulate dioxins) in seawater and mass of dioxins sedimentation to the bottom of the bay were calculated by the models. Results were compared to the published observation data in order to examine applicability of the used models. From the analyses, it was estimated that 23.30% of the dioxins inflow into the bay is deposited onto the bottom and that 69.46% flow out of the bay. Dioxins sedimentation is greater in the inner and middle parts of the bay and decreased in the direction to the bay entrance. Estimated dioxins concentrations in the sediment show a good agreement with the observed data.