1. Nearly hundred biological methods are used to assess the ecological status of European lakes within the Water Framework Directive (WFD) but still no study has compared their effectiveness to respond to different types of environmental pressures and to assess lake ecological status. 2. By using survey information collected in a questionnaire addressing authorities in all countries implementing the WFD, complemented by a literature review, we compared methods’ suitability to assess lake ecological status and their ecological rationale for the following biological elements: phytoplankton, benthic diatoms, macrophytes, benthic invertebrates and fish. 3. Our results showed that the definition of reference conditions for European lakes was overall based on existing near-natural reference sites, except for fish methods, although some of these sites were not validated with proper pressure criteria. 4. Multimetric methods were commonly developed with predominance of sensitivity/tolerance metrics for benthic diatoms, macrophytes and benthic invertebrates methods, an equal use of abundance and productivity and sensitivity/tolerance metrics for phytoplankton and a more balanced use of different metric categories for fish. 5. Biological elements showed different response to pressures which may be due to different life history traits and monitoring traditions for each biological community. The assessment methods based on phytoplankton seem to be the most effective since they showed the best response to eutrophication and had class boundaries primarily based on ecological rationale rather than statistical or expert judgment approaches. Statistics and expert judgment based approaches dominated in setting the quality class boundaries for macrophyte, benthic invertebrates and fish methods. 6. Current available methods are biased towards the detection of eutrophication, while hydromorphological pressures are seldom detected. 7. Effective restoration measures that are sufficient to achieve good ecological status in European lakes will require a better understanding of the response to pressures, particularly where other pressures than eutrophication dominate, and the use of more ecologically-based approaches in the boundary setting of all assessment methods. ; JRC.H.1-Water Resources