Floods, major formative drivers of channel and floodplain structure and associated riparian and in-stream communities(1,2), are increasing in intensity and magnitude with climate change in many regions of the world(3,4). However, predicting how floods will affect stream channels and their communities as climate changes is limited by a lack of long-term pre-flood baseline data sets across different organismal groups. Here we show salmon, macroinvertebrate and meiofauna communities, monitored for 30 years in a system evolving owing to glacier retreat, were modified significantly by a major rainfall event that caused substantial geomorphic change to the stream channel. Pink salmon, reduced to one-tenth of pre-flood spawner densities, recovered within two generations. Macroinvertebrate community structure was significantly different after the flood as some pioneer taxa, which had become locally extinct, recolonized whereas some later colonizers were eliminated. The trajectory of the macroinvertebrate succession was reset towards the community structure of 15 years earlier. Meiofaunal abundance recovered rapidly and richness increased post-flood with some previously unrecorded taxa colonizing. Biotic recovery was independent of geomorphological recovery. Markedly different responses according to the organismal group suggest caution is required when applying general aquatic ecosystem theories and concepts to predict flood events.