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This work focuses on an integrated approach for lake ecological status assessment, elaborated according to the requirements of the European Water Framework Directive (WFD). Data from five lowland and semi-mountain lakes in Bulgaria (Southeast Europe) collected from two years (2011-2012) form the basis for an integrated assessment and the definition of reference conditions. Several metrics were applied in combination, to classify lakes into five ecological status classes. Assemblages of aquatic organisms: phytoplankton, macrophytes and benthic macroinvertebrates, together with 11 supporting physico-chemical parameters were studied. The assessed unique conditions suggested that reference conditions of Bulgarian lakes have natural variability. This first baseline study illustrated specific cases within the lake types that should be assessed in details before providing standardized classification systems in compliance with the requirements of WFD.