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Ria de Aveiro represents a coastal territory, in which its natural capital, mostly classified under a Natura 2000 network of protected areas, is of paramount importance for the regional and national economy, supporting harbour activities and maritime traffic, agriculture, commercial fisheries, aquaculture, manufacturing, tourism, sports and recreational activities. Current and foreseen changes connected to human activities, namely land and water uses and potential conflicts, in frame of environmental policies, sustainable economic development and human wellbeing require the implementation of ecosystem-based management (EBM) planning processes considering the connectivity across marine, transitional, freshwater, and terrestrial domains. The main objective is to elaborate on the co-development of the EBM planning process across the three water domains, all characterized by high biodiversity and by the wide range of services provided by ecosystems and their abiotic components, for the mitigation of impacts from the management plan under implementation. The approach used follows a stepwise procedure in frame of resilience principles, considering the analysis of the relationship between the social and ecological components and on how these can be connected through risk assessment and a spatial multi-criteria analysis based on the delivery of ecosystem services. Stakeholders' perception matched the ecosystem services provisioning risk assessment and supported the planning EBM response that consist in saltmarshes and seagrasses meadows restoration programs. Compliance of the proposed measures is achievable regarding policies (policy targets and policy instruments) and feasibility (scientific and technological knowledge and financial resources). The EBM response can support the Vouga estuary management plan and regional smart specialization (RIS3 Centro). (c) 2018 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license.