Over the last decades, the combined effects of global climate changes and severe land use modifications have been exacerbating river hydrological alterations and habitat fragmentation in many Mediterranean rivers. This trend is predicted to intensify, with expected significant impacts on taxonomic and functional diversity of benthic communities in the next future.By comparing perennial and intermittent reaches, the present research aims at investigating the role of flow intermittency, driven by the combined effects of climatic variables and land use changes, on benthic diatom communities in Mediterranean streams (NW Italy), by analysing data collected over 11 years. In order to avoid potential confounding effects related to water quality, sites characterized by “poor” or “bad” water quality were excluded a priori.We observed significant differences between permanent and intermittent sections in terms of both climatic variables and land use: higher temperatures and lower precipitations, coupled with an extensive anthropic land use, intensify the natural flow intermittency in intermittent sites. This led to a significant decline in diatom species diversity, at both local and regional scales, and to changes to life history traits. In particular, communities of intermittent reaches were taxonomically and functionally different and less heterogeneous than assemblages characterizing perennial ones, showing higher percentages of small, mainly stalked and pioneer taxa belonging to the low profile guild. Conversely taxa colonizing permanent reaches were bigger, belonging to the high profile guild and able to produce colonies, thus indicating high environmental stability.Our results highlighted how hydrological alterations are profoundly threatening Mediterranean streams and the diatom communities inhabiting them, therefore representing an important benchmark in view of the improvement of biological indices for the assessment of intermittent rivers.