To predict the influence on fish stocks which were caused by environmental change in the fishing ground of shallow sea areas, we have developed the Shallow-Sea Ecological Model(SSEM) which that focuses on living organisms, especially fish and benthos. By applying the SSEM in the Seto-Inland Sea of Japan, we have simulated another aspect of influence on fish stocks that was caused by oxygen deficient water mass and nutrient loads. From the simulated result of the fish stocks, it was indicated that the stock of fish and benthos has shown a relative difference between the western sea and the eastern sea in the Seto-Inland Sea. According the to prediction, results of fish stocks that were caused by oxygen deficient water mass, it was estimated that the pelagicfish stock increases about 6 %, whereas the stocks of demersalfish and benthos decreases about 30% and 70%, respectively. On the other hand, it seemed that there was an increased in the fish stocks of demersalfish and benthos in the eastern sea of Seto-Inland Sea by nutrient loads reduction