Recently, forest ecosystem has faced various disturbances such as global warming, increasing nitrogen deposition, intensive grazing by herbivorous mammals, insect attacks, and so on. These disturbances will cause not only the loss of biodiversity, but also the alteration of nutrient cycling. To elucidate the complicated effects of various disturbances under natural condition, long-term researches are necessary. We examined biomass and primary production of trees, nitrogen deposition and loss to stream in a headwater catchment of a cool-temperate natural forest in northern Kyoto for 20 years. From 1990 to 2002, nitrogen deposition doubled and stream water nitrate concentration increased over 4 times. Nitrogen deposition was approximately constant since 2002, while a gradual increase in stream nitrate concentration to 2007 and then a gradual decrease was found. Primary production were constantly increased from 1992 to 2004, but they decreased since 2004 partly because of extensive dieback of Quercus crispula driven by ambrosia beetle. Under the condition that nitrogen deposition was constant, the increase in stream nitrate concentration and loss is suggested as the cause to Q. cirspula dieback. Its effect, however, continued for only a few years, which can be caused by compensation of Criptomeria japonica growth for the dieback.