Hydropower-based electricity production provides approximately 33% of renewable energy in Greece - an activity, however, associated with adverse environmental effects on watercourses. Therefore, it should be considered as a key factor of water management programs ensuring safety and optimising environmental performance of hydropower facilities in accordance to Greece’s obligations towards European Union (EU) water policy. Water Framework Directive (WFD) was created by the EU in order to help member states to protect and improve the status of water bodies and was incorporated in Greek legislation by Law 3199/2003 . Within the scope of this study, we assessed both Hydroelectric power generation and Water Resources Management in Greece and we recorded the current status of the EU Water Framework Directive implementation in this field. Given that social-ecological systems emphasise the link between people and the ecosphere, we investigated possible conflicts that arise between hydropower-related renewable electricity production and water courses conservation, according to both national and EU legislation. We also studied the tools that WFD provides in order to solve potential problems, maintain economic viability and ensure good ecological status between hydropower utilisation and water protection in the face of increased demands to a more effective and sustainable management of environmental resources.