The changes on community structures of benthic macroinvertebrates, relevance to the environment and interrelationship between benthos were studied over two years in stream with large environmental disturbance, which caused by localized heavy rain during Typhoon Chaba in October 2016. As a result, the number of species and individuals were increased after localized heavy rain, especially numbers of individuals of Ephemeroptera and Plecoptera were greatly increased. On the contrary, those of Semisulcospira libertina and Semisulcospira forticosta of Mesogastropoda were greatly decreased. Dominant species was Baetis fuscatus of Ephemeroptera, numbers of species and individuals of Ephemeroptera, Plecoptera and Trichoptera(EPT group) were dramatically increased from 26 species, 110 individuals to 32 species, 365 individuals respectively. This suggests that the change of river bed and flow velocity due to heavy rain provided a suitable environment for the EPT group that preferred the rift of a stream. In the functional feeding group, only gathering collectors and filtering collectors were identified in autumn of 2017 because some functional groups preferentially adapted to the changed environment. The interspecific competition and environmental condition were the worst in autumn after heavy rain due to the increase individuals of some species. The ecological score of benthic macroinvertebrate community(ESB) was higher after the heavy rain than before. Results of the Group Pollution Index(GPI), Korean Saprobic Index(KSI) and Benthic Macroinvertebrate Index(BMI) were similar to those before and after heavy rainfall. Therefore, ESB was the most discriminating method for estimating the biological water quality in this study. Some species that are sensitive to water quality changes still appear or increase individuals in the area under investigation after the heavy rain. On the other hand, the individuals of some pollutant species decreased. This is thought to be because the habitat fluctuation caused by heavy rainfall has improved the water environment.