The growing realization of the inadequacies of the conventional approach to climate change adaptation has generated interest in sustainable forms of adaptation that could promote long-term ecosystem health and social equity. In this regard, the concept of ecosystem-based adaptation has been receiving attention as an integrative framework for maintaining healthy ecosystems, with the aim of building the resilience and reducing the vulnerability of social–ecological systems to climate change impacts. However, there is currently an inadequate understanding of the institutional requirements for the transition towards ecosystem-based adaptation. A promising institutional mechanism for addressing these governance challenges is adaptive governance, a governance mechanism that relies on flexible, multi-level institutions to connect actors across multiple scales in managing conflicting values and uncertainties in ecosystem-based management processes. This paper discusses four roles of adaptive governance in the transition of water resource systems towards ecosystem-based adaptation: (1) creating awareness about climate change through social learning and the integration of diverse sources of knowledge; (2) generating interest for policy change through the provision of economic and non-economic incentives; (3) creating opportunities for change through the promotion of vertical and horizontal interactions among actors; and (4) building capacities for change through enhanced access to relevant institutions and resources.