We developed a numerical model, which consisted of hydrodynamic and ecosystem parts, to describe changes in dominant species of red-tide phytoplankton in Tokyo Bay. Phosphorus flux from the land to the bay in 1974 was 1.8 times as large as that in 2001, and the mole ratio of Si/P during 1974-2001 rose from 9.7 to 19.5. These are consistent with observed phytoplankton succession that diatom is predominant over nondiatom plankton. We confirmed the model accuracy of hydrodynamic part from agreement between the calculated and the observed results on sea temperature, salinity, and nutrient concentrations. A numerical simulation under the inflow condition of the low Si/P ratio was carried out. The results showed that the growth of the non-diatom plankton increased with the decreasing Si/P ratio.