ABSTRACT1. Mediterranean freshwater ecosystems are among the most endangered by global change. In order to design appropriate conservation policies it is essential to ascertain which are the most vulnerable freshwater habitats.2. Aquatic Ranunculus communities are used as target habitats to answer the following questions: (a) Does regional climate influence the distribution of aquatic plant communities? (b) Do nutrient enriched and base-rich waters act as a filter for aquatic habitats, reducing the number of plant communities? and (c) Is the European Habitats Directive classification for freshwater habitats that support Ranunculus species fit for purpose?3. The floristic consistency of nine Ranunculus communities and their affinity with freshwater ecosystem types was analysed. A study was made of the relationships between environmental factors, including climate and aquatic physico-chemical parameters, and the composition of Ranunculus communities. Significant environmental parameters were analysed separately to define the ecological niche occupied by Ranunculus species.4. At a regional scale, climatic variables best explain the distribution patterns of the Ranunculus communities, and separate Atlantic communities (Ranunculus tripartitus, R. omiophyllus, R. ololeucos and R. fluitans communities) at localities with a higher rainfall/temperature ratio from the rest. At a local scale, a strong relationship was found between the distribution of Ranunculus communities and physico-chemical properties, in the following order of importance: alkalinity, flow, and nutrient status. Hard waters reduce Ranunculus community richness to a R. trichophyllus community, and waters enriched by phosphates to a R. penicillatus community.5. The rainfall/temperature ratio, alkalinity, and eutrophication shape the vegetation composition in Mediterranean freshwater habitats. In view of this, some gaps were identified in the European Habitats Directive with regard to Atlantic and oligotrophic base-poor freshwater habitats.