A key barrier to achieving Ecosystem-Based Management (EBM) is dealing with complexity of social-ecological systems (SES). SES incorporate ecological, social and economic factors that interact within and between each other. Carrying out quantitative analyses to aid decision making in these systems is often too complex and/or limited by data. We describe a complementary approach, the use of Linkage Frameworks, that can be used to explore EBM. Linkage frameworks are essentially networks of elements or nodes found in a system, with links representing the interactions between those nodes. In an EBM context, nodes might include human activities, their pressures, biodiversity components, the ecosystem services supplied in that ecosystem, and the users or beneficiaries of the activities and services supported. Interactions could highlight, for example, which activities introduce which pressures, which biodiversity components are linked to which human activities through their pressures, and which ecosystem services are supplied by each biodiversity component. This approach can help to structure systems conceptually, allowing consideration of complex systems in decision making and facilitating communication between, for example, scientists, ecosystem managers and stakeholders. We discuss the strengths, assumptions and limitations of the tool, drawing on examples from aquatic ecosystems across Europe. Lessons Learned • Although dealing with the complexity of SESs can be challenging, there are advantages to persevering. We show, using a linkage framework approach, that retaining the complexity of the system in analyses to inform decision making, can provide different perspectives on EBM questions. • Linkage Frameworks are specified for specific systems and specific issues or problems. It is important that users are aware of this as the specification will affect the understanding of the system.