The enactment of the Water Framework Directive (WFD) initiated scientific efforts to develop reliable methods for comparing prevailing lake conditions against reference (or nonimpaired) states, using the state of a set biological elements. Drawing a distinction between impaired and natural conditions can be a challenging exercise, as it stipulates the robust delineation of reference conditions along with the establishment of threshold values for key environmental variables used as proxies for the degree of system impairment. Another important aspect is to ensure that water quality assessment is comparable among the different Member States. In this context, the present paper offers a constructive critique of the practices followed during the WFD implementation in Greece by pinpointing methodological weaknesses and knowledge gaps that undermine our ability to classify the ecological status of Greek lakes. One of the pillars of WDF is a valid lake typology that sets ecological standards transcending geographic regions and national boundaries. The national typology of Greek lakes has failed to take into account essential components (e.g. surface area, altitude, salinity).
WFD compliance assessments based on descriptions of phytoplankton communities areoversimplified and as such should be revisited. Exclusion of most chroococcal species from the analysis of cyanobacteria biovolume in Greek lakes and most reservoirs in the Mediterranean Geographical Intercalibration Group (Greece, Spain, Portugal and Cyprus) is not consistent with the distribution of those taxa in lakes. Similarly, the total biovolume reference values and the indices used in their classification schemes reflect misunderstandings of WFD core principles. This hampers the comparability of ecological status across Europe and leads to quality standards that are too relaxed to provide an efficient target especially for the protection and management of Greek/transboundary lakes such as Lake Megali Prespa, one of the oldest lakes in Europe.