In recent years aquatic macrophytes have come into the focus of interest as useful biological indicators for the assessment of ecological quality in lakes in the context of the implementation of the EU Water Framework Directive (WFD). Introducing this thesis an overview of past and recent scientific activities related to this subject in Europe is given. The main focus of the thesis was on the development of a WFD-compliant assessment system for macrophytes in Austrian lakes. With a multi-metric approach different aspects of the macrophyte vegetation are considered, allowing the detection of eutrophication or re-oligotrophication processes as well as of impacts by shore embankment, artificial wave action and water level fluctuations. In order to compare assessment results derived from such methods all over Europe the WFD stipulated a so called “intercalibration exercise”. The results achieved in the Lake Macrophyte Alpine Geographical Intercalibration Group (Alpine-GIG), lead by the author, confirmed sufficient comparability of the Austrian, French, German, Italian and Slovenian assessment systems. During the lake investigations Najas flexilis, a macrophyte species new for Austria was found. Since Najas flexilis is listed in Appendix 1 of the Bern Convention and the Annexes II and IV of the European Habitats Directive, this record is also highly important for the development of the Europe-wide species protection plan. In the context of the WFD macrophyte studies, the development of a new mapping method for large lakes as well as the establishment of a macrophyte-based typology for Austrian lakes were required, as described in this thesis. Additionally, results from the first detailed macrophyte investigation in an Austrian lake, (Lake Attersee; Pall 1994) are taken as an example to illustrate possibilities for describing and evaluating macrophyte vegetation data with the aid of different numerical indices.