Aquatic macrophytes can serve as useful indicators of water pollution along the littoral of lakes. In Bavaria, the submerged vegetation of about 100 lakes has been investigated by SCUBA diving over the past decade to evaluate the state of nutrient pollution. All lakes are marl lakes located in the northern calcareous alps and the prealpine region. The lakes differ in size, morphology, water residence time, nutrient loading, trophic status, recreational activities, and other characteristics. In all cases the entire shoreline of the lakes has been investigated. Among the investigated lakes are the three biggest Bavarian lakes, i.e. Lake Chiemsee, Lake Starnberg and Lake Ammersee. Mapping of the submerged vegetation occurred in four different depth zones, and variable shoreline sections. The length of each section was determined by the uniformity of the vegetation; as it changed, a new section was designated. Within each section and zone species were recorded and abundance of all observed macrophytes was estimated semi-quantitatively on a five-point scale. Nine different groups of macrophytes were recognised, including, in total, 45 different species of macrophytes. On the basis of this catalogue of indicator species, in combination with the abundance of the species, a 'macrophyte index' was devised, which ranges from 1 (unpolluted) to 5 (heavily polluted). Six groups of values of the macrophyte index, each represented by a different colour or grey-scale (in this publication), are presented to allow a clear illustration of the results. Important information for the successful restoration of lakes in Upper Bavaria has been obtained from the distribution patterns of the submerged vegetation. Many unknown waste water inflows or diffuse sources could be detected due to abrupt changes in the macrophyte index. Furthermore, the success of waste water removal by 'ring canalisation', resulting in a re-oligotrophication of many Bavarian lakes can be followed by changes in the macrophyte index.