Stable isotope approach for aquatic ecology and environmental sciences has been introduced as very useful technique since 1980s and also has been applied to investigate various issues in aquatic ecology and environmental study last 10 years in Korea. Especially carbon and nitrogen isotope ratios have been mainly used to understand food web energy flow and ecosystem structure. In addition, nitrogen isotope ratio has been applied for nitrogen cycle and source identification as well as biomagnification studies. However, large temporal or spatial variations of nitrogen isotope ratio of primary producer have been found in many aquatic environments, and it is regarded as the critical problems to determine trophic level of aquatic animals. Recently, the compound specific isotope analysis of nitrogen within individual amino acids has been developed as an alternative method for trophic ecology. This article introduces the progress history of stable isotope application in aquatic ecology and environmental sciences, and also suggests new direction based on future prospects in stable isotope ecology and environmental study.