A structured and collaborative approach to design and decision-making in the context of ecological restoration of rivers is developed and illustrated using a case study involving the mitigation of physical barriers to fish migration on the River Trent in the UK. The integrated design and decision-making framework provide a practical workflow model for structuring multi-attribute decisions, engaging stakeholders, and assembling a design team needed to successfully plan environmental interventions. In our implementation team members included ecologists, fisheries biologists, government scientists, and representatives of key stakeholder groups. The case study demonstrated a values-based approach to implementing an ecological restoration plan that addresses some of the long-standing barrier removal goals associated with the reintroduction of Atlantic salmon and European Union (EU) Habitats Directive listed species European lamprey and River eel. The integrated decision-driven, design framework approach is highlighted by trans-disciplinarily and social learning.