This paper presents the results of the FLUMAGIS project, in which we developed a spatial decision support system (SDSS) to support the implementation of the European Water Framework Directive (WFD). The modelling approach is based on the integration of ecological and socio-economic assessment methods, scale-specific and GIS-based data and knowledge modelling and visualization techniques. The project study area is the intensively cropped Upper Ems River Basin in north-western Germany. A method was developed that enables the transfer of scale-specific data and information. Analyses were performed for baseline conditions and specific management and planning scenarios to improve water quantity and quality at micro-, meso- and macro-scale. The results of the study indicate that substantial, expensive water and land management changes at different scales would be necessary to achieve the WFD water quality targets in this basin. Ecological-economic analysis of cost-effectiveness reveals that the costs of achieving certain goals of the WFD can vary more than tenfold depending on which measure is chosen out of the pool of management alternatives. Moreover, the study shows that the differentiation between landscapes and other regional characteristics although considered essential to the successful implementation of WFD measures is very data intensive.