The determination of the environmentally minimum water level in lakes is crucial, as it provides water managers with a tool for the protection of lake ecosystems, although, it could also start a conflict with water uses. The assessment of minimum level is quite challenging and depends on biotic and abiotic factors, related to biological communities and hydromorphological features of the lake ecosystem. Herein, a hydromorphological method is presented for assessing the minimum lake level using the water level-volume relationship and the annual inflow of surface water into the lake. In addition, a hydrological evaluation of the assessed minimum level is applied to ensure that the minimum level could be safely used by water managers over a range of wet or dry hydrological years. The hydromorphological method is demonstrated in three lake ecosystems of Northern Greece, where the minimum level has also been estimated with other methods, based on a morphological analysis and on water level requirements of macrophytes species. The hydromorphological method is straightforward and provides estimations of minimum lake level that satisfy the key requirements of species.