Long-term nitrogen (N) loading on forest ecosystems can lead to “N-saturated forest”. Such an ecosystem is likely to have high nitrate (NO₃^-) concentrations in mountain stream water and leach more N than the input of N deposition. Recent increases in atmospheric emissions from livestock and agriculture have also disturbed the N biogeochemical cycle in terrestrial ecosystems. We investigated NO₃^- concentrations in 200 water samples from forested catchments of the Miyazaki region and assessed the relationship between stream NO₃^- concentration and the amounts of N deposition and catchment properties (e.g., climate, topographic factors, vegetation, geology, and soil) using Random Forest (RF) Regression. Stream NO₃^- concentration ranged from 0.01 to 1.07 mg-NL^-1 indicating that N retentions of the catchments were variable in the study area. The results from the RF regression model show that the annual precipitation, N deposition based on ammonia (NH₃) emissions from livestock and agriculture, and annual N concentration in deposition can be key factors regulating NO₃^- leaching from the forested watersheds. Other important factors regulating stream NO₃^- concentration are temperature, elevation, and solar radiation of the catchments. It is the first time to show the influence of livestock and agriculture activity on the mountain stream chemistry in Japan.