Nitrogen compound deposition as a result of human activities on the terrestrial surface has increased sharply during the last one hundred years, causing ecological problems. One problem is nitrogen saturation in forest ecosystems, which results in the forest ecosystem receiving more nitrogen than required. In recent years, nitrogen oxide emissions have been decreasing in Japan; however, the total deposition of nitrogen is not decreasing because of cross-boundary emissions from other countries. As depositions in forest ecosystems increase, the likelihood of nitrogen saturation increases. At the same time, certain species of trees, geological conditions, and climate will affect nitrogen saturation. In Japan, there is heavy precipitation in summer; therefore, decreases in nitrate concentrations of stream water cannot be observed. Stable isotope analysis is the key to elucidating nitrogen dynamics between the atmosphere and rivers. From the atmosphere to stream water, nitrogen compounds have many chemical and biological reactions. Because a stable isotope is an indicator of the progress of these reactions, frequent analyses of stable isotope compositions reveals how nitrogen moves from the atmosphere to stream water.