Recent concern about the potential danger to ecosystems posed by the environmental pollutions has focused attention on the mobility of various solutes, especially nitrate and organic matters, in relatively shallow hydrologic systems. Also utilization of isotopic tracers is a promise strategy to describe the origin, pathway and transformation of water, nutrients and other substances moving with water. In this talk, I will show a recent trend and novel techniques of isotopic applications to elucidate hydrological characteristics and biogeochemical reactions in catchment ecosystem. The deuterium excess value which is calculated from δ²H and δ¹⁸O of rainwater sampled in the Japanese Archipelago has usually remarkable seasonal variation with high in winter and low in summer, because of the evaporative conditions of original water vapor. This seasonal variation can be used to estimate the residence time of various waters stored in catchment processes. The δ¹⁵N and δ¹⁸O of dissolved nitrate can give us the information on the origins and transformations of nitrate in a catchment. These multiple isotopic characterizations of hydrological and biogeochemical dynamics are required to reveal more detailed insights of the water and nutrient cycle in catchment ecosystems under various types of anthropogenic and natural disturbances.