Since the construction of Isahaya Dyke, it is said that the tidal current in Ariake Bay has changed. The change may bring on the environmental deterioration in Ariake Bay. Especially in Isahaya Bay and the offshore of Oura, the emergence of oxygen-deficient water has been prominent. In this study, firstly, we simulated the emergence of oxygen-deficient water by incorporating an ecosystem model into an ocean current model to elucidate the mechanism of the oxygen-deficient water both from physical and biological viewpoints. Next, we proposed a local engineering solution, a seawater-quality enhancer, and simulated numerically the diffusion of nutrient-rich water emitted by the apparatus and its effects on the ecosystems, particularly, on the oxygen-deficient water. The apparatus spreads horizontally the intermediate-density mixture of surface and deep waters. The numerical model considered 8 principal rivers because the nutrient-rich density currents of fresh water largely affect the currents and the ecosystems in Ariake Bay. It was shown that 16 % of the oxygen-deficient water in Isahaya Inlet was reduced by the apparatus, which emits 100-million-ton water per day, at 8 weeks after the start of operation. This may imply the possibility of improvement of water quality by this engineering countermeasure.