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Several mountain streams are currently changing from perennial to temporary regimesdue to increasing water abstraction and global climate change with expected detrimental effects on stream biodiversity and functionality. We here examined whether macroinvertebrates and diatoms, experiencing recurring non-flow periods, showed alterations even after complete flow resumption in 13 mountain streams in SW Italian Alps. Benthic communities were sampled after complete flow resumption in April 2017 in a control section, with permanent flow, and inan intermittent section, which experiences recurrent non-flow periods during summer, in each stream. We tested for differences in terms of taxonomic composition, diversity and functional groups between permanent and temporary sections. Our results showed a significant alteration of benthic invertebrate, but not diatom communities in temporary sections. Different species composition and low diversity values in temporary sections were due to the replacement of monovoltine taxa, with aquatic respiration, preferring medium to fast flowing, oligotrophic waters by plurivoltine taxa, with aerial respiration preferring lentic habitats. Such results provide some insights into the mechanisms by which non-flow periods impact Alpine streams, and further investigations in mountain areas are required in the future to better unravel the repercussions on stream ecosystem processes.