The objective of this study was to develop a hydro-chemical model using the Soil and Water Assessment Tool (SWAT) and to evaluate the climate change impacts on discharge and nitrate-nitrogen loads from Ise Bay watersheds (the Kiso, Nagara, Ibi, and Shonai rivers). Using a regional climate model, through the dynamic downscaling approach, present and future climate data were generated at a 2 km spatial resolution. The pseudo-global warming downscaling approach under the A1B scenario was adopted for future climate prediction. Then, the optimized SWAT model, driven by the present and future climate data, was executed. The following results were obtained: (1) the significant increase of precipitation in May and June and decrease in August in the future climate scenario, and consequent discharge from the target watersheds also increased in May and June and decreased in August and September; (2) Due to the change in discharge, nitrate-nitrogen loads of the Kiso, Nagara, and Ibi rivers also increased in May and June and decreased in August and September; and (3) While nitrate-nitrogen load from deciduous forest tends to decrease, the one from evergreen forest tends to increase. The response of the model indicated the possibility of an increase in nitrogen uptake by deciduous forests.