The application of stable isotope analysis has contributed to visualizing the food web as a two-dimensional plot based on carbon&nitrogen stable isotopes, and it has made quantitative analyses possible for isotopic niche space, which can assess the amount of available resources, the degree of resource distribution to organisms, and biological interaction that occur during the resource utilization process. In the case of higher-trophic fish, analyzing their isotopic niche spaces and evaluating the degree of their overlap can be used as a composite indicator of lower-trophic organisms’ responses focused on biological interactions to environmental changes. In this study, we analyzed the isotopic niche space and overlap of fish community classified by feeding group in four large river system with different environmental condition using R software packages; SIBER& nicheROVER. Furthermore, in order to quantitatively evaluate the organisms’ responses to natural and artificial environment changes, the correlation between environmental factors and Layman’s community indices is statistically analyzed based on isotope niche to identify the response of each fish feeding group according to habitat-environmental characteristics. The results of this study are believed to contribute to identifying impacts of aquatic ecosystem disturbances, including rainy season, on the fish community in terms of structure and function.