The aquatic macrophytes of lakes, situated in the whole territory of Bulgaria, were monitored during 2009. Six lake groups were established using differences in characteristics reflecting altitude, high calcium content and salinity, and altered hydromorphology and/or artificial origin. Abundance and species composition were assessed at each lake according to the requirements of the EU Water Framework Directive, using the assessment procedure of macrophyte-based assessment system, proposed by the Bavarian Environment Agency. The procedure included calculation of the ‘ecological quality ratio’ (EQR) for each of 78 water bodies, based on transect monitoring data. For 31 of these lakes, a macrophyte assessment system was applied, for the remaining 47 lakes macrophyte quantity was insufficient or depopulation was assessed. Ecological status classification of lakes is based on the calculation of a Reference Index value. The Reference Index quantifies the deviation of species composition and abundance from reference conditions and classifies sites as one of the five possible ecological quality classes specified in the Directive. The EQR indicating Good and High (Maximum) Ecological Status/Potential for macrophytes was achieved in 12 of the 31 lakes which fulfilled the criteria for assessment. The water quality parameters in lake types were discussed.