Recently, many member states of the European Union (EU) have finalised and implemented national systems for water quality assessment in lakes according to the EU Water Framework Directive (WFD). It is however unknown how the assessment of ecological status, according to the WFD, relates to the status of lakes according to the EU Habitat Directive (HD). High ecological status according to the WFD should mean high status according to the HD. To avoid any conflicts between different EU directives and national environmental objectives, surface waters protected as for example Natura 2000 sites should ideally show high ecological status according to the WFD. Also, high ecological status according to the WFD should imply the presence or potential for presence of red-listed species. Here, we studied the ecological status of 1014 Fennoscandian lakes (224 Norwegian, 491 Swedish and 299 Finnish lakes) according to the WFD and related it to the number of red-listed species per lake and to the status of the lakes as Natura 2000 areas. High ecological status according to the WFD did not mean high status according to the HD or according to national environmental objectives. In general, the number of red-listed species decreased with increased ecological quality ratios. In Norway 47%, in Sweden 78%, and in Finland 29% of lakes with red-listed species were classified as lakes of moderate or worse ecological status according to the WFD. In Sweden 39 of 68 studied Natura 2000 lakes had a moderate or poor ecological status according to the WFD. In Sweden and Norway, in contrast to Finland, macrophyte-based assessment systems are primarily a trophic index, i.e. penalising lakes with elevated phosphorous concentrations. The multimetric nature of the Finnish index probably contributes to the better agreement between the WFD assessment and the number of red-listed species in Finland compared to Sweden and Norway. In Sweden six of eight red-listed species occur in lakes with phosphorous concentrations considerably above reference conditions. Generally, it is assumed that biodiversity is favoured by intermediate nutrient concentrations. In addition, instead of phosphorous, Ca concentrations appear important for the occurrence of many redlisted species, especially for Charophytes. Rapid revision of the national indices is needed to increase compatibility between the two EU directives and to increase the agreement between the WFD and national environmental objectives.