Europe’s four regional seas (Baltic, Black, Mediterranean and NE Atlantic) have suffered severe environmental degradation due to human pressure. Existing measures to manage pressures have proven inadequate and the EC has responded by proposing a new policy (Maritime Strategy Blue Book) and environmental legislation (Marine Strategy Directive), both currently close to adoption. These instruments rely on the Ecosystem Approach, a management paradigm that encompasses humans and the supporting ecosystem. But the science base for this approach needs strengthening and practical tools must be developed and tested for policy implementation. In particular, criteria for assessing costs and benefits of management actions are poorly developed, particularly in the complex marine environment where multiple uses and management conflicts are common. The KnowSeas consortium will strengthen the science base for managing Europe’s seas through the practical application of systems thinking. It will work at the two scales envisaged for emergent EU policy: the Regional Sea Scale and Member State Economic Exclusive Zones (EEZs). We have developed a new approach of Decision Space Analysis to investigate mismatches of scale. Knowledge created through the FP6 European Lifestyles and Marine Ecosystems project, augmented with necessary new studies of climate effects, fisheries and maritime industries - in EEZ case studies - will provide a basis for assessing changes to natural systems and their human causes. New research will examine and model economic and social impacts of changes to ecosystem goods and services and costs and benefits of various management options available through existing and proposed policy instruments. Institutional and social analysis will determine conflicts of interest and examine governance as well as stakeholder values and perceptions. Our research will develop and test an assessment toolbox through regional liaison groups and a multisectoral Project Advisory Board.