We tested the applicability of two available Water Framework Directive (WFD) compliant phytoplankton indices on three large peri-alpine lakes to analyze their suitability for trophic classification. We show that the indices vary in their final resulting Ecological Quality Ratios (EQRs) and are only appropriate to roughly distinguish lakes of different water quality according to OECD criteria (OECD, 1982). Annual mean TP concentration in Lake Geneva was 0.03 mg l-1 in 2006 (Lazzarotto & Rapin, 2007), which marks mesotrophic conditions. According to the tested indices, the lake is of ‘good’ (0.60–0.80) quality after the GermanWFDmethod (PSI) and of ‘moderate’quality according to the Austrian WFD method (BI).We prove that the way how to derive the per annumvalue of the metric ‘Brettum Index’ (BI) in the Austrian WFD method significantly influences the resulting index and the scatter of long-term data. We focused on improvement strategies for this index in terms of calculation and sampling frequency. Contrary to the tested bin, the modified index presents no significant differences between four and six sampling dates per year. In order to improve the significance of the available indices, we propose to modify the way of per annum index calculation for the AustrianWFDmethod as well as to focus on species composition to achieve a high relative proportion of indicator species. A phytoplankton index alone may not be sensitive enough to track the changes that occur within a lake. The results confirm the need to take into account other biological elements such as fish, macrophytes, attached diatoms and macrozoobenthos as suggested by the WFD.