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Climate change is predicted to increase drought occurrence and severity in small continental watercourses. Here, we studied the structure and the functional diversity of benthic diatom assemblages in lowland intermittent and permanent watercourses of the Carpathian Basin. We assumed that the community structure of intermittent and permanent watercourses would be markedly different, and the functional diversity in both would be strongly influenced by autumn drought. We found that intermittent streams were primarily characterized by small-sized generalists and aerophilic taxa, while permanent watercourses were inhabited by large-sized planktic or fast moving groups. The functional richness was significantly lower in intermittent than in permanent streams. This decrease in the functional richness of benthic algal communities may negatively affect the functioning of lotic algal communities. We conclude that diatom assemblages in lowland intermittent watercourses are sensitive indicators of changes in ecosystem properties, and should be considered in appropriate evaluation and management of extreme climatic events on aquatic ecosystems.