We analysed the response of fish communities to hydropeaking (frequency, magnitude, ramping rate and timing) and the interaction with the habitat conditions in Austrian rivers. An index of biotic integrity (Fish Index Austria) was used to compare river sections with varying degrees of flow fluctuations under near-natural and channelized habitat conditions. The results showed that habitat conditions, peak frequency (number of peaks per year), ramping rate (water level variation) and interaction between habitat and ramping rate explained most of the variation of the Fish Index Austria. In addition, peaking during the night seems to harm fish more than peaking during the day. Fish communities in hyporhithral and epipotamal types of rivers are more affected by hydropeaking than those in metarhithral type of rivers. The results support the findings of other studies that fish stranding caused by ramping rates >15 cm h−1 are likely to be the main cause of fish community degradation when occurring more often than 20 times a year. While the ecological status degrades with increasing ramping rate in nature-like rivers, fish communities are heavily degraded in channelized rivers regardless of the ramping rate. The mitigation of hydropeaking, therefore, requires an integrative approach considering the combined effects of hydrological and morphological alterations on fish. © 2014 The Authors. River Research and Applications published by John Wiley & Sons, Ltd.