Phytoplankton is the most suitable quality element for assessing the ecological status of standing surface water bodies such as lakes and reservoirs. In order to evaluate changes in these water bodies, it is important to determine the reference areas (REFS) and maximum ecological potential areas (MEPS) so as to explain the deviations from the reference conditions and maintain or improve the ecological condition of the water bodies. This study explains the methodology used in the designation of the REFS and MEPS based on the phytoplankton quality element in inland surface waters by the Project for the Establishment of a Reference Monitoring Network in Türkiye. For this purpose, a total of 275 lakes and reservoirs were investigated in three sampling periods and at several sampling points according to lake size from eight basins in 2017, nine basins in 2018 and eight basins in 2019. The evaluation of phytoplankton was mainly based on phytoplankton and cyanobacteria biovolumes. Phytoplankton biovolume metrics (PT-BV and CY-BV) have been developed for the sampled shallow and deep standing water bodies. A total of 79 lakes and reservoirs from eighteen typologies were determined as REFS and MEPS according to phytoplankton. In addition, the approaches and precautions taken to protect the reference areas are explained.