Although the important roles of flood disturbance in maintaining the integrity of riverine ecosystems are well known, there still exits much uncertainty in the resilience of biota to events with an unprecedented magnitude under future climate change. Rivers and their adjacent riparian zones are connected to each other via across-ecosystem energy flows, and thus need to be understood as an integral entity. There are, however, very few studies about the effects of extreme high-magnitude floods on biota, and assessments of biota simultaneously both in rivers and riparian zones. This study examined flying arthropod responses to a flood with a record-breaking high-water level in August 2016 in Eastern Hokkaido. Samples were collected at four sites before (April to July 2014) and after (April to October 2017) the flood along the riparian forest of Satsunai River, a tributary of the Tokachi River. The flood caused variable responses in different orders of arthropods. Hymenoptera, Coleoptera and Lepidoptera which almost entirely inhabit in terrestrial habitat significantly decreased by 52.1%, while other aquatic Ephemeroptera, Plecoptera and Trichoptera exhibited negligible responses. Higher resilience of aquatic taxa may reflect their higher adaptations to physical disturbance of habitat though exposures to frequent lower-magnitude floods.