Climate change is causing frequent and large floods, creating a need for information regarding the impact of severe flood disturbances on stream invertebrates. We briefly describe the response of invertebrate assemblages to an extreme flood event in 2018 in the western Ehime Prefecture of Japan. We compared invertebrate data collected in past regional-scale surveys with those gathered by revisiting 27 study sites after the flood and examined the relationship between catchment characteristics and the invertebrate response across the study area. Heavy rainfall was recorded in the catchment of each study site during the flood (range 565–1081 mm). Stream invertebrates may be eliminated by the historical flood, although the degree was small compared with that in previous reports on the effects of severe flood disturbances (abundance − 19.1%, taxon richness − 9.0%), likely owing to the absence of severe bed disturbance. Our results imply that high primary productivity, possibly caused by low elevations and the development of farms, accelerated the recovery of invertebrates after the disturbance. They also suggest that assembling pre-disturbance data is the key to understanding the impact of extreme floods on stream invertebrates and managing stream ecosystems during climate change.