The recent definition and submission of WFD-compliant River Basin Management Plans required large efforts of water managers and highlighted a number of data, knowledge and methodological gaps that need to be fulfilled during the next management cycle. The complexity of the WFD implementation process calls for easy-to-use, reliable and scientifically sound decision support tools that consider relevant aspects of the basin of concern. For this purpose, a Decision Support System (DSS) for risk-based assessment and management of river basins was developed within the EU MODELKEY project. The MODELKEY DSS allows assessing the chemical and ecological status of water bodies by applying both the One-Out All-Out principle, suggested by the WFD, and a novel Integrated Risk Assessment (IRA) methodology, developed within the project.