The intensification of catchment land use and the corresponding habitat degradation poses a threat to freshwater quality, quantity, biodiversity, and ecosystem health. Hence, the Water Framework Directive (WFD) commits all European Union members to achieve good ecological status of all water bodies and spell out procedures. The main focus of this research is to validate nutrient stress boundaries based on the ecological quality ratio (EQR) with diatoms as stipulated by the WFD for rivers in Hungary. The main objectives include determining whether the rivers in Hungary meet good biological status using their EQR phytobenthos; determine whether there is a good correlation between EQR-phytobenthos and some selected physical and chemical parameters; and establishing nutrient stressor boundary for good ecological status of rivers in Hungary. Knowledge about the nutrient stressor boundaries will equip water resources managers and planners with accurate and secure information that will enable them to develop the required interventions and management practices to ensure the proper functioning of freshwater ecosystems.