Distribution of aquatic organisms is governed by various environmental factors Hydromorphological characteristics which are heavily affected by heavy rains in stream are one of the fundamental factors to influence the distribution of aquatic organisms. In this study we evaluated the difference response of two aquatic species Chironomus yoshimatisui and Limnodrilus hoffmesteri habiting to changes of discharge due to heavy rains. We compared the differences in their resilience and recover to disturbances. Our results showed that after a heavy rain during the sampling periods, the proportion of macrosubstrate highly increased and was not recovered into the previous states. Nonmetric Multi-dimensional scaling based on Chironomidae and Oligochaeta biota well represented annual and seasonal differences with heavy rain effects. Random forest model showed that the abundance of C. yoshimatisui were mainly influenced by microsubstrate, precipitation and Reynolds number, whereas stream roughness, mesosubstrate and macrosubstrate much more influenced the abundance of L. hoffmesteri.