A numerical study by means of a marine ecosystem model is conducted to examine the causes of change in the marine environment of Tokyo Bay in the latest 70 years. First, the marine ecosystem model is validated by comparing the predicted water quality such as water temperature, dissolved oxygen (DO), chemical oxygen demand (COD), total phosphorus (T-P) and total nitrogen (T-N) for the year of 1994 with the field data, which has been observed at 48 spots in Tokyo Bay. In addition, topography of Tokyo Bay and the discharge of chemical matters from the rivers are estimated for each year of 1935, 1979, and 1994, and the marine environment in the summer of each year is reproduced by numerical simulation. From comparing the results, it is revealed that the marine environment varies corresponding mainly to change in the discharge of chemical matters, and that the impact of reclamation is about 30% of the impact of change in the discharge of chemical matters.