A large variety of plant species of very different evolutionary origin are found within and along the margins of aquatic ecosystems. These species have very different adaptations depending on the particular environmental condition under which they grow. This thesis examines the role of these adaptations or functional traits for the distribution on large scales and along specific environmental gradients. Characean algae (charophytes) are an ancient group of aquatic plants found in most aquatic ecosystems. I confirmed that they have declined markedly during the 20th century, most likely as a consequence of widespread eutrophication, and that declining species were characterized by traits such as being obligate perennial and having preference for alkaline lakes. Partly as a consequence of this, there was an exceptionally high proportion of rare charophyte species in Denmark and Scandinavia. Theses rare species are specialists in particular environments, while the abundant species have traits such as broad salinity tolerance, tall shoots, vegetative reproduction and variable life form. Vascular plants, in contrast to charophytes, occupy the entire gradient from submerged to drained conditions. Along this gradient their functional traits vary markedly due to the environment conditions filtering away species lacking suitable adaptations. I found that the filtering of traits was highly dependent on specific traits and position along the gradient and the traits experiencing the strongest environmental filtering also proved to be the most important in predicting the species composition under local conditions. The results stress the importance of environmental filtering as mechanism determining community assembly in plant communities. The zone from submerged to drained conditions along the margins of softwater, oligotrophic lakes is often dominated by isoetids. They have the remarkable adaption of using sediment CO2 taken up through permeable roots. This trait makes isoetids vulnerable to sediment anoxia caused by degradation of organic sediments following eutrophication. I investigated if sediment desiccation leads to high mineralization without stressing the plants. The sediment mineralization increased following desiccation and plants continued to grow well under drained, fluctuating and submerged conditions stressing the potential use of desiccation as a sediment restoration tool in eutrophied systems. In conclusion, species functional traits have a large influence on distribution of species both on large scales and along specific environmental gradients.