The European Union has adopted several environmental directives, strategies, recommendations, and agreements that require a shift from local- or regional-based regulations to more ecosystem-based, holistic environmental management. Over the next decade, environmental management in Europe is likely to focus more on biological and ecological conditions rather than physical and chemical conditions, with ecosystem health at the center of regulation and management decision making. Successful implementation of this new ecosystem management and strategic assessment process in Europe will require the integration of regulatory and technical information and extensive collaboration from among European Union member countries, between agencies, and across disciplines to an unprecedented degree. It will also require extensive efforts to adapt current systems of environmental assessment and management to the basin and ecosystem level, across media and habitats, and considering a much broader set of impacts on ecosystem status than is currently addressed in most risk assessments. This will require the understanding, integration, and communication of economic, ecological, hydrological, and other processes across many spatial and temporal scales. This article discusses these challenges and describes some of the research initiatives that will help achieve integrated ecosystem management in Europe.