In the Ariake Sea, dike construction in Isahaya Bay in 1997 for reclamation and disaster prevention was thought to cause big anthropogenic impacts on the marine ecosystem. Currently, hypoxia or anoxia occurs every summer in Isahaya Bay and the inner Ariake Sea. However, the effects of the dike construction on the DO concentration are unclarified. The present study evaluated the impact of the dike construction on the DO concentration by applying a numerical ecosystem model. The present calculation showed that the dike construction could affect the DO concentration in summer in a wider area than reported before in the steady state with a neap-spring tidal cycle. In Isahaya Bay, the dike construction caused a decrease of DO concentration greater than 2.0 mg l−1 , due to the decrease in DO supply from the vertical diffusion process with reduction of tidal current and the intensification of the density stratification. The dike construction also affected the DO concentration in the inner Ariake Sea by decreasing the DO concentration of the water transported by the estuarine circulation and the reduction of the diffusive supply of oxygen vertically with stratification enhanced by the dike construction. For the first time, this study showed with numerical simulation that the dike construction could affect the DO concentration in a wide area of the Ariake Sea.