Today, climate change, together with other anthropogenic influences is considered as a major threat affecting aquatic ecosystems in several ways. Here, altering water contraction (standing and flowing phases) and human-induced habitat variability (natural and artificial stream sections) were studied as modifying factors driving community changes in benthic diatom assemblages of a Hungarian small lowland stream (Létai-ér). We assumed notable compositional differences between phases and habitats, but we expected these differences to decrease with drying. Moreover, lower diversity was hypothesized in assemblages of both artificial section and flowing phase. While taxonomic composition did not reveal significant differences between the sections, well pronounced compositional changes were found between phases. Surprisingly, no significant diversity changes were observed during water contraction. Compared to the natural microhabitat, however, artificial stream section was found to maintain more diverse diatom community. These results emphasize that modification effects of climate change induced hydrological extremes can lead to remarkable compositional changes in benthic algal assemblages even on a short time scale, that must be taken into account in both water management and nature conservation strategies.