To predict the risk of combined acidification and deoxygenation in eutrophic waters and evaluate the effectiveness of measures to reduce anthropogenic CO₂ emissions and terrestrial nutrient loads as countermeasures, we developed a high-resolution coupled ocean physical and biogeochemical model for Tokyo Bay, a representative eutrophic water body in Japan. It has been reported that dissolved oxygen (DO) concentrations in the bottom waters of Tokyo Bay occasionally fall below the threshold for adverse impacts on commercially important species such as the coastal demersal fish Sillago japonica, and future projections show that if anthropogenic CO₂ emissions and nutrient loads from rivers remain at current levels, the adverse impacts on these target species will intensify. On the other hand, if nutrient loads from rivers are reduced, the number of days on which DO concentrations fall below the adverse impact threshold for Sillago japonica would actually decrease. It was quantitatively demonstrated that in Tokyo Bay, which receives a high nutrient load, reducing nutrient inflow from rivers would have an effect on future combined acidification and deoxygenation impacts comparable to that of curbing global CO₂ emissions.