The environmental protection of tropical marine and coastal areas faces different challenges due to the diversity of aspects related to these areas, which include natural, social and economical issues. Despite these challenges, efforts for the protection of these areas are urgent nowadays because of the dramatical increase of human related threats like habitat destruction and population growth. Malaga Bay (MB) is a tectonic estuarine system located in Panama Bight (central region of the Colombian Pacific coast), which due to its origin shows important environmental characteristics of few sites in the Tropical Eastern Pacific (TEP) match. For these reasons, the government of Colombia declared in 2010, the bay’s marine area as a Marine National Natural Park in order to preserve its unique estuarine marine biodiversity. Despite this measure, MB presents several conditions that make environmental protection a very difficult task. In this paper, we present the geographical context, biodiversity and natural resources, environmental threats, the complexity of economic and social context, and the institutional and legal context of MB, to exemplify the difficulty that the protection of marine areas face in the TEP.