Mediterranean watercourses are among the most threatened ecosystems worldwide, being increasingly important to understand environmental drivers of biotic assemblages. Our aim was to provide a comprehensive picture of bryophyte communities in Mediterranean rivers and to determine the environmental factors that influence their distribution. We used floristic data collected for inter-calibration purposes under the European Water Framework Directive and River Habitat Survey, from 474 river reaches in six countries of the European Mediterranean basin. We analysed data through classification, ordination and environmental niche modelling techniques, and classified taxa according to biogeographic and aquatic habitat frameworks developed specifically for bryophytes. These analyses revealed four types of communities influenced by spatio-temporal precipitation patterns, altitude and water chemistry factors, most notably calcium and manganese. Community types are compositionally differentiated, although they share some core taxa and show an overall tendency to have several temperate and exclusively aquatic taxa despite the intermittent nature of water flow in highly seasonal Mediterranean rivers. The modelling approach can be improved at a more local scale when more bryological data and higher-resolution environmental information become available. Given future scenarios of climate change and human alteration of hydrological regimes, broader scales studies are needed to monitor shifts in bryophyte communities. © 2016 Springer International Publishing Switzerland

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