The EU Water Framework Directive (WFD), establishing stringent quality objectives for European basins in the next years, prompts for the development of new tools to evaluate and improve the ecological status over European rivers. The present paper will provide an overview of the main activities carried out in the DECIS subproject within MODELKEY, an European research project, funded by the European Commission, aimed to contribute to the assessment, understanding and prediction of the impacts of environmental toxicants on biodiversity in aquatic ecosystems. The main aim of DECIS is to develop a Decision Support System (DSS) that includes all project deliverables (i.e. exposure and effect models; key toxicants identification tool), and integrates Ecological Risk Assessment (ERA) with socio-economic valuations. In fact, DECIS specific objectives are: development of integrated risk indexes, ranking and prioritization of hot spots at basin scale, estimation of ecological risks at site-specific scale, definition of monitoring programs based on ERA results, performance of socio-economic analysis at the basin scale, technical development and application of the new DSS to three representative European case-studies (Schelde, Llobregat and Elbe). The framework of reference for the development of the DSS is presented taking primarly into consideration EU regulatory frameworks. Moreover, possible links with other existing models and DSSs for river basin management are discussed.