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Enclosed coastal seas and wetlands are areas of high ecological value with singular fauna and flora, but several cases of environmental catastrophes in recent decades can easily be referenced in the international literature. The management of these natural territories is complex in developed countries since they are usually subjected to intense human activity with a varied catalog of activities and anthropizing features that alter the balance of the ecosystem. In this article, the concept of the Socio-Ecological System (SES) to diagnose and achieve a sustainable cohabitation between human anthropization and the natural values based on the tool of GIS participatory mapping is proposed as an innovative approach for the management and recovery of these complex areas. The article develops a comprehensive general methodology of spatial GIS diagnosis, planning, and co-management implementation between public and private stakeholders combined with economic tools such as the Willingness to Pay (WTP) and the Cost Transfer Sector (CTS). This innovative approach is applied to the Mar Menor lagoon, which is an international and successful case study of environmental recovery on the Spanish Mediterranean coast. The coastal lagoon suffered an unprecedented eutrophication crisis in 2015, but it managed to recover in the summer of 2018 without the need to implement major structural measures. In this case study, several solutions to redress the current impacts will be developed through a participatory process based on GIS mapping. Lastly, the discussion reflects the concept of self-resilience of an ecosystem based on the unexpected positive turn of the environmental crisis in the lagoon ending. Full article