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Strategic environmental assessment (SEA) is used to identify the potential impacts of plans and policies such as maritime spatial planning (MSP). Studies have demonstrated ambiguity in SEA objectives and substantial knowledge gaps in existing and emerging SEA practices for MSP. The aim of this paper is to support a methodology for the development, implementation, and monitoring of SEA for MSP plans based on a stepwise, participatory mapping exercise by experts, using indicators to evaluate areas of conflicts/synergies in possible future scenarios. An overview of 16 proposed indicators identified a representative criterion. Participatory sector analyses were performed in three scenarios. Most conflicts focused on coastal areas, indicating that coastal planning should be a priority in all possible scenarios. The methodology developed in this paper uses GES indicators to perform the assessment of the three different scenarios and makes the development of a participatory mapping approach with experts in the very early stages of the process a more feasible alternative for a first assessment. This methodology was efficient in a collaborative SEA evaluation of MSPs to facilitate an ecosystem approach in an Azorean case study.