Ecosystems of suburban landscapes (i.e., forest, inland water ecosystem) are threatened by high nitrogen (N) loadings derived from urban air pollutants. Forest ecosystems under high chronic N loadings tend to leach more N via streams. In the northern suburbs of Tokyo, N deposition loading on terrestrial ecosystems has increased over the past 30 years. In this region, we investigated nitrate concentrations in 608 independent small forested catchment water samples from northeastern suburbs of Tokyo. The nitrate concentrations varied from 0.07 to 3.31 mg-N L-1 in this region. We evaluated the effects of N deposition and catchment properties (e.g., meteorological and topographic factors, vegetation and soil types) on nitrate concentrations. In the random forest model, simulated N deposition rates from an atmospheric chemistry transportation model explained most of the variance of nitrate concentration. To evaluate the effects of afforestation management in the catchment, we followed a model-based recursive partitioning method (MOB). MOB succeeded in data-driven identification of subgroups with varying sensitivities to N deposition rate by vegetation composition in the catchment. According to MOB, the catchment with dominant coniferous coverage that mostly consisted of plantation with old tree age tended to have strong sensitivity of nitrate concentrations to N deposition loading.