From a comprehensive diagnosis of the associated basins, islands, and wetlands of the coastal lagoon system of Ciénaga Grande de Santa Marta, Colombia, this work describes feasible options for the recovery of its ecosystem’s health and ecological resilience. Firstly, the state of the coastal lagoon was assessed, finding that hydrology, wave climate, and the morphological changes of the coastline explain recent changes in the coastal wetlands. Key variables were used to describe the level of conservation or degradation of the coastal lagoon system and to identify measures to improve its ecological functions. Finally, to mimic some of these functions and improve connectivity of the ecosystems, green infrastructure alternatives were proposed for the short and medium term to recover the services of these ecosystems and restore their resilience.