This article addresses the theoretical and practical challenge faced by the European policy community and Member States trying to simultaneously pursue renewable energy and environmental goals, as incorporated in the EU Renewable Energy Directive and the Water Framework Directive. Through the case of hydropower, which is today at a crossroads between being a renewable electricity source − answering to climate change and energy security concerns − and a local environmental challenge in the light of degradation of river ecosystems and local biodiversity, the article explores the way renewable energy and water protection objectives are integrated inside the Common Implementation Strategy at the EU level. Based on document analysis and interviews, the mapping of the different frameworks shows that old conflicts and controversies related to the hydropower technology have been reopened and reframed to accommodate both the issue of energy security and the discourse on EU sustainability and climate change. Conclusions reveal that despite the creation of a multi‐stakeholder platform for negotiation and collaboration, the Common Implementation Strategy fails on several occasions to explain how to achieve the right balance and leaves unclear what specifically has to be integrated and to what degree. Hence, given the plurality and diversity of values, interests and concerns in relation to hydropower and goals of the Water Framework Directive, a prioritization between water, climate and energy policy goals might be needed, with the possibility of having real winners and losers of the integration process. Copyright © 2016 John Wiley & Sons, Ltd and ERP Environment