Without doubt, taxonomy is the basis for studies in ecology and biodiversity, and is thus an essential prerequisite for limnology. As aquatic biodiversity is threatened by human impacts on a global scale, so the "species" Homo sapiens var taxonomicus is threatened by the new educational strategies of most universities. This special issue on macrophyte distribution in the Danube and selected tributaries of the entire river basin represents an important milestone within the scientific community. The work presented has value both in terms of basic science and in management application, and sets a new standard for aquatic plant investigations. It provides an inventory of macrophytes that are indicators for water quantity (e. g. flow regimes altered by hydropower dams, hydrological connectivity in floodplains), water quality (e. g. eutrophication), as well as providing habitat for other aquatic life, such as invertebrates, benthos and fish. The standardization of methods enables a sound comparison between different study sites as well as an interpretation of long-term changes such as the dynamics of succession and the invasion of neophytes. The application of analytical tools such as geographic information systems (GIS) and predictive models for determining the impact of human activities on plant communities provides an excellent basis for future river management and restoration strategies promoted by the International Commission for the Protection of the Danube River and guided by the European Union's Water Framework Directive.