In this research, the effect of human activities has been investigated in the Ariake Sea located in Kyushu Island. Japan. The Ariake Sea has been suffering from environmental degradation for more than a decade with unstable fisheries productivity. Therefore, it is important to understand the change of environmental characteristics in the Ariake Sea quantitatively. Moreover, it is concerned that the fertilizer applied for the aquaculture is effecting to the ecosystem in the sea. Also, since nutrient loading from rivers are so high that red tide or anoxic water mass occurs every year, it is significant to evaluate the effect of nutrient load to the sea. Therefore, in order to characterize the coastal environment and investigate the effect of human activities, Muti-Box Ecosystem model have constructed to simulate the water quality items in the Ariake Sea. The sea was divided into 12 boxes. Each box is comprised of three layers which is water, oxidative bottom and reductive bottom layer. Simulation period was set from 1st January 2000 to 31st December 2012. The model reproduced the water quality items well. Then, the model calculated with two different scenarios about the fertilizer application to the aquaculture and nutrient load from the river. The result showed that the fertilizer for the aquaculture has no effect to the coastal ecosystem and coastal environment would improve if the nutrient load reduced by half.