Social-Ecological Systems (SESs) are systems with close linkage between nature and societies. Coastal lagoons are SESs crucial for the ecosystem services (ESs) provided, especially in the Mediterranean Basin, facing threats from anthropogenic activities and climate change. Management strategies focusing solely on ecological elements’ improvement have not yielded the desired outcomes, as they often neglect the needs and perspectives of stakeholders. Participatory approaches promote engagement and awareness to develop sustainable and effective management strategies. Aiming to contribute to the preservation and sustainable management of the Nestos Delta coastal lagoons, a Natura 2000 site in Greece, this study explores the application of intuitionistic fuzzy sets (IFS) to capture the inherent uncertainty in stakeholder opinions against complex environmental challenges. Through this participatory approach, stakeholder perspectives were assessed and quantified to rank management alternatives. Ecological health and economic values were prioritized, endorsing the adoption of natural and soft interventions; conflicts and a knowledge gap regarding non-provisioning ESs were revealed, highlighting the necessity of inclusive consultation processes. This approach offers the potential to facilitate consensus-building and enhance the legitimacy of coastal lagoon management decisions.