In this article, focusing on the ongoing implementation of the EU Water Framework Directive, we analyze some of the opportunities and challenges for a sustainable governance of water resources from an ecosystem management perspective. In the face of uncertainty and change, the ecosystem approach as a holistic and integrated management framework is increasingly recognized. The ongoing implementation of the Water Framework Directive (WFD) could be viewed as a reorganization phase in the process of change in institutional arrangements and ecosystems. In this case study from the Northern Baltic Sea River Basin District, Sweden, we focus in particular on data and information management from a multi-level governance perspective from the local stakeholder to the River Basin level. We apply a document analysis, hydrological mapping, and GIS models to analyze some of the institutional framework created for the implementation of the WFD. The study underlines the importance of institutional arrangements that can handle variability of local situations and trade-offs between solutions and priorities on different hierarchical levels.