Main distribution patterns of submerged macrophytes in a large number of Danish lakes were determined and relationships to environmental variables evaluated by different multivariate analysis techniques. The lakes varied greatly in location, size, depth, alkalinity and trophic status. There were distinct differences in the distribution of species and growth forms among the lakes. The lakes separated into five groups of characteristic species compositions. Alkalinity was the main factor responsible for the species distribution. Lakes of high alkalinity were dominated by vascular plants of the elodeid growth form, lakes of intermediate alkalinity contained a variety of elodeids and vascular plants of the isoetid growth form, while lakes of low alkalinity and low pH had several isoetids and bryophytes, but very few elodeids. Alkalinity is a close descriptor of the bicarbonate concentration, which is an important source of inorganic carbon in the photosynthesis of many elodeids. The species distribution was related to their ability to use bicarbonate and extract inorganic carbon, implying that the observed distribution has an eco-physiological foundation, though a substantial variation suggests an influence of phenotypic plasticity and local environmental heterogeneity. Trophic state also influenced the distribution of species, with very eutrophic lakes having only a few robust elodeid species able to compensate for turbid conditions, while small elodeids and slow-growing isoetid species were absent. The distance separating the lakes did not influence similarity in species composition among them.