Without sustainable rehabilitation measures, the Lobau, a freshwater Biosphere Reserve, will soon became a primarily terrestrial ecosystem with major implications for its rich aquatic and amphibic biodiversity. An innovative ecosystem management scheme for this Danube floodplain needs to optimally balance between conservation and restoration objectives and to harmonize the partly competing ecologic and socio-economic requirements for the next 40 years. Therefore, we present a project dealing with the development of a multi-criteria Decision Support System (DSS), based on interdisciplinary historical analyses and state-of- the-art ecosystem modelling. The DSS will assists multiple stakeholders in finding coherent and realistic management alternatives, by linking all objectives and measures in a transparent and reproducible way.