Floods are a key component of the flow regime of many rivers and a major structuring force of stream communities. Climate change is predicted to increase the frequency of extreme rainfall (i.e. return intervals >100 years) leading to extensive flooding, but the ecological effects of such events are not well understood. Comparative studies of flood impacts are scarce, despite the clear need to understand the potentially contingent responses of multiple independent stream systems to extreme weather occurring at meso- and synoptic spatial scales.We describe the effect of an extreme rainfall event affecting an area >100 000 km2 that caused extensive flooding in SE Alaska. Responses of channel morphology and three key biological groups (meiofauna, macroinvertebrates and fish) were assessed in four separate and recently deglaciated stream catchments of contrasting age (38–180 years) by comparing samples taken before and after the event.Ecological responses to the rainfall and subsequent flooding differed markedly across the four catchments in response to variations in rainfall intensity and to factors such as channel morphology, stream sediment composition and catchment vegetation type and cover, which were themselves related to stream age.Our study demonstrates the value of considering multiple response variables when assessing the effects of extreme events, and highlights the potential for contrasting biological responses to extreme events across catchments. We advocate more comparative studies to understand how extreme rainfall and flooding affects ecosystem responses across multiple catchments.