Ongoing coastal development and the prospect of severe climate change impacts present pressing estuary management and governance challenges. Robust approaches must recognise the intertwined social and ecological vulnerabilities of estuaries. Here, a new governance and management framework is proposed that recognises the integrated social-ecological systems of estuaries so as to permit transformative adaptation to climate change within these systems. The framework lists stakeholders and identifies estuarine uses and values. Goals are categorised that are specific to ecosystems, private property, public infrastructure, and human communities. Systematic adaptation management strategies are proposed with conceptual examples and associated governance approaches. Contrasting case studies are used to illustrate the practical application of these ideas. The framework will assist estuary managers worldwide to achieve their goals, minimise maladaptative responses, better identify competing interests, reduce stakeholder conflict and exploit opportunities for appropriate ecosystem restoration and sustainable development.