Charophytes play an important role in aquatic ecosystems but there is a lack of knowledge on the ecology of these macroalgae. Our aim was to characterize the habitat of 12 charophyte species from 78 sites in Switzerland characterised by a set of environmental variables considered critical to the physiology and survival of these plants (climate, land-use, morphometry and chemistry). We searched (i) to evaluate how environmental gradients explain the distribution of species; and (ii) to identify if some species have narrower habitat range than others (“specialist” vs “generalist” species). The Outlying Mean Index (OMI) measures the distance between the mean habitat conditions used by a given species and the mean habitat conditions of all studied waterbodies and was used to analyse the distribution of species. Waterbody size, conductivity and altitude were the most discriminating habitat variables of 7 of the 12 species, followed by calcium and total phosphorus. Chara strigosa is considered a specialist of cold oligotrophic hard waters, and three as generalists (C. contraria, C. globularis, C. vulgaris) with respect to our set of charophyte sites. We demonstrate that charophyte species occur together in a narrow environmental envelope but do not occupy exactly similar habitats. Despite a discrepancy among absolute optima of species in different countries, the relative position of species is likely to be transferable to other regions. Improving our understanding about the ecology of charophyte species by considering a broader scale dataset and more fine-scale biotic and abiotic factors is proposed as an important perspective.