The purpose of this study is to evaluate the future climate change impact on stream aquatic ecology health of Han River watershed (34,148 km2) using SWAT (Soil and Water Assessment Tool) and random forest. The 8 years (2008~2015) spring (April to June) Aquatic ecology Health Indices (AHI) such as Trophic Diatom Index (TDI), Benthic Macroinvertebrate Index (BMI) and Fish Assessment Index (FAI) scored (0~100) and graded (A~E) by NIER (National Institute of Environmental Research) were used. The 8 years NIER indices with the water quality (T-N, NH4, NO3, T-P, PO4) showed that the deviation of AHI score is large when the concentration of water quality is low, and AHI score had negative correlation when the concentration is high. By using random forest, one of the Machine Learning techniques for classification analysis, the classification results for the 3 indices grade showed that all of precision, recall, and f1-score were above 0.81. The future SWAT hydrology and water quality results under HadGEM3-RA RCP 4.5 and 8.5 scenarios of Korea Meteorological Administration (KMA) showed that the future nitrogen-related water quality in watershed average increased up to 43.2% by the baseflow increase effect and the phosphorus-related water quality decreased up to 18.9% by the surface runoff decrease effect. The future FAI and BMI showed a little better Index grade while the future TDI showed a little worse index grade. We can infer that the future TDI is more sensitive to nitrogen-related water quality and the future FAI and BMI are responded to phosphorus-related water quality.