The present study explores the process of Greece’s current decarbonisation transition and its energy policy regarding the country’s two coal-mining areas. Using the Region of Western Macedonia as a case study, we aimed at providing a holistic approach—as until now only few attempts have been made to systematise the ‘Just Transition Plans’ in European Union (EU)—for raising awareness on issues related to water resource management in post-lignite areas and analysing the use of hydropower in Greece. Our research draws on a flexible method approach, serving as a tool to identify gaps in current knowledge and practices, based on two stages—first the analysis of existing literature, reviews, and sources from government’s core strategies, as well as policy and decision-making papers, and then formulating research questions by synthesising relevant data. In Greece, both ‘Just Transition Development Plan of Lignite Areas’ and hydropower production practices overlook water resources management. By summarising our findings and identifying gaps that remain in current approaches, this work indicates future directions by suggesting processes necessary for addressing the complex issue of adoption of sustainable water resources management measures in post-lignite eras in accordance with EU’s water policy.