Prediction formula of the number of upstream migration in the Yodo River in Japan, was constructed using chlorophyll-a in Oct (X1) and sea water temperature in Feb (X2). Y=89340X1-288402X2+2579513. Impacts of climate change on the number of Ayu-fish migrating upstream in the Yodo River was also assessed under CMIP3 climate models by developing distributed hydrological model which calculate river discharge and temperature. Under the A1B scenario, future mean water temperature at the river mouth from January to March increase by about 2 degrees and the future number of upstream migration is estimated to decrease. As a mitigation measure of increasing water temperature by climate change, lowering temperature of the sewage treatment water that flows into river is found to be effective based on a comparison between heat flux from the sewage treatment water inflow to river and increment heat flux in river by climate change.