The Water Framework Directive (WFD) structures long-term plans for Europe's threatened water resources. Owning to the inherent and human-made complexities of the water cycle, stakeholders must move strategically to avoid crisis and restore sustainability. Yet, the reality of water resource management today is falling short on delivery. Stakeholders require strategic tools that will help them to build consensus and take action in the right direction. Using the Framework for Strategic Sustainable Development (FSSD), this study shows how Decision Support Systems can be strategically improved using a whole-systems approach grounded in basic Principles for Sustainability. In this way, stakeholders will be capable of making synchronized moves towards sustainability and thus more likely to realize the WFD’s goal of ‘good status’ for all European waterways by 2015.