The Yatsushiro Sea has serious environmental problems similar to those affecting the Ariake Sea. In this study we performed a causal analysis of environmental change in the Yatsushiro Sea by investigating environmental characteristics such as water quality and atmospheric phenomena over the past 26 years. Numerical experiments yielded the following results: 1) there exist 5 distinct environmental domains within the Yatsushiro Sea, 2) during summer, density layers develop over the entire Yatsushiro Sea, and 3) an increase in the activity of red tides and a recent decrease in nitrification capacity indicate a decrease in oxygen content within the inner part of the Yatsushiro Sea.A three-dimensional flow simulation produced the following results: 1) the characteristics of the tidal current in the Yatsushiro Sea are related to those of the Ariake Sea, and 2) current drift has decreased more in the inner part of the Yatsushiro sea than in the southern central part. The results of this study indicate significant ongoing change in the water environmental characteristics of the Yatsushiro Sea.