1. Thirty-six species of macrophytes (fourteen flowering plants, two quillworts, sixteen mosses and liverworts, and two algae) were collected in an extensive survey of 116 high mountain lakes in the eastern Pyrenees. Seventy per cent of the lakes showed macrophyte development. 2. The isoetids (Isoetes lacustris, Isoetes setacea and Subularia aquatica) were the dominant growth form, although the natopotamid Sparganium angusifolium was the most widespread species. Potamids (Potamogeton spp., Ranunculus spp.), the alga Nitella gr. opaca and some mosses (Warnstorfia exannulata, Sphagnum denticulatum) were often present. 3. A multivariate ordination analysis (RDA-redundancy analysis) revealed that water chemistry, altitude and vegetation cover of the catchment, and nutrient availability are major environmental factors associated with macrophyte distribution along the eastern Pyrenean lakes. Isoetids prevailed in softwater oligotrophic lakes, potamids in relatively hardwater oligotrophic lakes, and Potamogeton natans and Callitriche palustris in small and eutrophic water bodies affected by the presence of cattle.