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Marine-coastal ecosystems are productive and valuable habitats worldwide due to their significant contributions to human wellbeing. However, human activities, limited territorial planning, and unsustainable demand and consumption of natural goods and services put pressure on marine-coastal ecosystems. In this sense, marine-coastal planning is a management tool to contrast these forces because it manages different human activities on the coast and in the oceans over space and time, strengthening political, social, and tourist development and the economy of the territory. Our objective is to propose marine-coastal spatial planning strategies through an ecosystem-based approach for allocating a mangrove and estuarine zone conservation area. The study methodology is: (i) Compilation of information from the study area with an emphasis on regulations and protected areas. (ii) Analysis of human relations with marine-coastal ecosystems. (iii) Mapping and zoning of the conservation area. (iv) Analysis of the strengths, weaknesses, opportunities, threats and threats, weaknesses, opportunities, strengths (SWOT–TWOS) matrix to recommend strategies and guarantee the viability of marine-coastal protection. The results show zoning maps of the sector proposed as a conservation area comprising mangroves and an estuarine zone. It also approaches governance strategies or conservation management measures and protection of the marine-coastal space. Finally, as a recommendation, we propose improvements to the current municipal ordinances, guaranteeing the management and protection of the study area, and furthering achievements in the comprehensive development of land-use planning.