As a laborsaving technique for weed control in a mountainous area in Japan, an integrated grazing system (IGS) for scattered small pastures has gathered attention recently. The objective was to estimate the loading doses of nitrate-N and ammonium-N in soils and agricultural water as result of this IGS approach compared with other land uses. As a result of time-course profiles of nitrate-N and ammonium-N in surface soils, the effect of applied fertilizers was emphasized more than the effect of manure produced by grazing animals. The nitrate concentrations of under-drainage from pasture were the same or lower than those of agricultural water below a vegetable field during grazing periods. It was considered that the IGS was at least the same or had a lower impact on N levels than that of vegetable fields.