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The extent of drought in Mediterranean streams has been intensifying recently, and the mean annual discharge is expected to experience a decreasing trend in coming years, with significant effects on aquatic ecosystems. The aim of this study was to analyse colonisation patterns of diatom communities that differed in terms of taxonomic composition and percentage of endangered taxa exploring the possible development of resistance mechanisms. To this end, we selected three Mediterranean streams comparable in terms of water quality, but different in terms of surrounding land use, and we performed two experimental treatments. The first treatment consisted in artificially drying and cleaning of substrates (cobbles) to analyse the post-drought recolonisation process that is only driven by drift and immigration. In the second treatment cobbles coming from a site experiencing a seasonal drought were transplanted upstream in a perennial stretch to explore the possible development of resistance mechanisms within diatom communities periodically exposed to droughts. We observed that stream identity played an important role in determining diatom assemblage composition. Highly natural stretches had a high abundance of endangered species, which were less resilient to drought than assemblages composed of general and widespread taxa. Moreover, according to our results, resistance mechanisms did not play a significant role in recovery patterns. Improving our knowledge of diatom resilience mechanisms is very important in a global climate change scenario, especially in Mediterranean streams.