At the end of 2000, the European Commission published its Water Framework Directive (WFD) in the Official Journal of the European Communities (2000/60/EC). This new legislation provides for achieving the sustainable management of water resources through its 26 articles that focus primarily on the improvement and protection of the quality of European water resources. The WFD adopts an integrated approach, based upon general principles deriving mainly from four disciplinary approaches, Geography; Ecology; Economics and Sociology. The new challenges posed to the people responsible for the management of water resources across the European Union include the "marrying" of existing national policies with the stipulations of the WFD. Research can support this transition by identifying compatibility and conflicts between legislative instruments, and by encouraging trans-national cooperative relationships. A relevant role of research is also foreseen in providing criteria and tools for conflict resolution by representing the goals of sustainable management in an objective and transparent way. The elaboration required for making planning decisions are increasing in number and complexity, requiring tools that help to organise and communicate the data that should be used to describe the decision context in terms of sustainability, in a holistic way by including environmental, economic and social information. These problems are being addressed by the MULINO Project, a 3-year research program aiming at producing a Decision Support System that will assist water managers in responding to the evolution of policies and management methodologies. The development of the system, which will be prepared in a software format, is being steered by a group of people from European water authorities. This steering committee is contributing to the policy analysis component of the research and to the software design which aims to be applicable in five different national contexts. This paper addresses the challenges and innovations that have been encountered in the second phase of research in which the first prototype of the software has been developed to operate in specific decision situations in each of MULINO's six case studies.