The dissertation is an analytical review of the available literature on marine protected areas (MPAs) to propose some governance, and spatial management mechanisms in the Colombian Caribbean Sea, particularly in the Seaflower MPA. The Seaflower MPA is facing several challenges regarding political issues of boundary disputes and also adverse impacts on the marine environment from the increase in shipping activities. This is largely due to the expansion of the Panama Canal and the possible Nicaragua Canal, which is increasing the maritime traffic of international shipping to almost double that of today. In addition, the increase in seabed activities is also a threat to the ecosystems within it. This research describes the Colombian framework of MPAs, and it also shows the issues that face the Seaflower MPA today. The aim is to propose and to recommend some governance and management measures based on the ecosystem-based approach to establish a transboundary agreement keeping the integrity of the MPA and giving regional relevance for the protection of the unique ecosystems. Furthermore, to address the issues of negative impacts from shipping, some protective measures have to be taken to protect the ecosystems and safe navigation guaranteeing long-term sustainable development.