Lake Sagami, which is fed by the Katsuragawa River, supplies about 60% of tap water in Kanagawa Prefecture. However, excess growth of phytoplankton due to high loading of nutrients such as nitrogen in summer has been an issue since the 1980s. Therefore, identifying nitrate loading in the Katsuragawa River watershed can be considered to be critical. The headstream of the river, at the northern foot of Mt. Fuji, is selected for a study of nitrate loading, in which oxygen, hydrogen, and nitrogen isotopes in water and nitrate are used to determine the sources of springs and nitrate contamination. Hydrogen and oxygen isotopes in water samples indicate that precipitation at the northern foot of Mt. Fuji and water from Lake Yamanakako are the main sources of springs in the Oshino area. Low nitrate concentrations with high nitrogen isotope values in spring water indicate low-level wastewater contamination in the springs. Furthermore, a watershed investigation identifies the characteristics of nitrate loading in the Katsuragawa River. The distribution of nitrate concentration and nitrogen isotope values indicates that springs and wastewater drainage from residential areas are significant sources contributing to the upstream nitrate load. However, nitrate concentrations and nitrogen isotope values downstream are reduced by the diluting effect of tributary water originating from mountain areas.