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Estuaries are one of the most productive and complex types of ecosystems supporting a wide range of economic activities. Departing from a set of governance problems and emergent goals, such as sustainability or climate change adaptation faced by an estuarine case study area, Ria de Aveiro, in Portugal, this article assesses the adequacy of alternative governance models under the existing water resources legal framework and traditional political culture. It shows that apart from the centrally-based compliance model, all other alternatives require high degrees of institutional reforms. Moreover, although the model based on a dedicated new agency, long preferred by many users of Ria de Aveiro, is the most understandable and focused, it does not assure the pursuance of adaptability or collaboration, which are considered essential for estuary governance. As it relies on collective action and multi-level and multi-agent contexts, estuarine governance may require a new institutional design. Where one begins a process of institutional change, however, is not a simple issue to address and demands a deeper analysis, particularly on the types of required institutional changes, as well as on their impacts on policy and decision-making outcomes over estuarine environments and associated socio-ecological networks.