It is widely known that water transparency is a simple but efficient indicator to monitor Mediteranean lakes, as it is strongly related to frequent disturbunces/stressors occuring in this climatic region, namely, intense warm periods, eutrophication, hydrological modifications and extended draught related to climatic variability. Twenty years ago, the Water Framework Directive (WFD) demanded from European Member States the establishment of physico-chemical thresholds for natural waterbodies. Our aim is to define water transparency boundaries for Greek natural shallow and deep lakes to assist water management and support the WFD good water quality goal. For this attempt, the official lake monitoring timeseries (period: 2013-2020, lakes: 8 shallow and 7 deep) of Secchi Depth (SD) and ecological quality ratios (expressed by all biological quality elements) were used. These were processed according to the “Best Practice Guide” utilizing the Shinny application (JRC) coupled with mixed statistical modeling (e.g., different types of linear regressions, box-plots, binary logistic regression). The results reflect the lake functioning and the multiplicity of pressures; thus, for shallow polymictic lakes, whose majority fails to achieve good ecological status, the proposed SD Good/Moderate boundary is stricter, while for the warm deep monomictic lakes with a better status, the boundary depicts the tolerance these waterbodies have. These findings are crucial tools for linking policy objectives to management actions, ultimately assisting restoration. The designation of data-driven boundaries for both shallow and deep Greek natural lakes offers multiple benefits. High-frequency SD measurents can assist in tracking water transparency and trophic status, perform as bloom warning systems, act as a proxy for hydrological parameters (i.e., residence time, flushing rate), monitor restoration projects' efficiency, capture the trend of climate change impact and guide lake management actions related to water uses (i.e., fisheries, tourism, recreation), while enabling local communities’ stewardship (via citizen science campaigns).