Nitrogen (N) is one of the essential elements for plant growth and plays an important role in biological activities in nature. In natural, N leaching out of forests, mainly in the form of nitrate (NO3-), is generally small. However, the present anthropogenic production of N has dramatically increased the N presence in forest ecosystems and it may lead to acidification in terrestrial ecosystems and eutrophication in aquatic ones. NO3- leaching from forests can be quite variable because it depends on various environmental factors. Therefore, monitoring approaches are needed for effective forest ecosystem conservation and management. This study aims to examine the local environmental factors influencing the water quality of forest streams in two regions. Stream NO3- concentrations were investigated for 200 forested watersheds from Miyazaki prefecture and 120 from Kagoshima prefecture. The random forest regression model, a machine learning technique, was used to identify the environmental factors influencing stream water chemistry. NO3- concentrations varied from 0.01 to 1.07 mg N L−1 in Miyazaki and 0.01 to 0.78 mg N L−1 in Kagoshima. This study will mainly discuss on the spatial distribution of forest stream water chemistry and the local environmental factors influencing stream water chemistry of two adjacent regions.