In Matsu-zawa catchment, central Japan, nitrate concentrations in stream water increased following a small-scale, natural disturbance involving an outbreak of pine wilt disease that affected ∼25% of the forested catchment. To clarify nutrient dynamics in soils and their relationship with stream water nitrate, we investigated soil nitrogen dynamics and soil water chemistry in disturbed and undisturbed, water-unsaturated and -saturated plots. The highest values for nitrification rate, nitrate concentration in soil solution, and nitrate exported from the root zone were observed for the disturbed plot. The ratio of nitrification to mineralization in surface soil of the disturbed plot dramatically increased from 1989 (pre-disturbance) to 1997. Root zone leachate from the disturbed area showed gradually increasing groundwater nitrate concentrations in the temporarily saturated zone during lateral, matrix flow. The catchment's deep soils and associated hydrologic processes limited the degree of plant uptake of the nitrate generated in the disturbed area. It was inferred that the persistent high levels of nitrate observed in the stream water resulted largely from the stable high nitrate concentrations observed in the saturated groundwater of this catchment. Stream water nitrate loads discharged following the disturbance were about 16 times greater than prior to it.