Parts of southern Guam are proteced areas designed to preserve threatened terrestrial, freshwater and marine habitats. There are several types of protected areas, and they are managed by different entities.

Marine Preserve Areas (MPAs) are coastal areas were fishing activity has been restricted in response of decreasing reef fish stocks. Of the five MPAs on Guam, two are located in southern Guam. Sasa Bay MPA covers inner parts of Apra Harbor and Achang Reef Flat MPA includes the large fringing reef on the northeastern fringe of Cocos Lagoon. The MPAs are managed by Guam Department of Aquatic and Wildlife Resources.

There are also two terrestrial conservation areas in southern Guam. Named Bolanos Conservation Area and Cotal Conservation Area, they were created to protect native flora and fauna in the interior of southern Guam. Both sites are dominated by savanna and ravine forests and both are managed by Guam Department of Aquatic and Wildlife Resources.

In addition, parts of the lands managed by the U.S. Navy are classified as "overlay" zones of the Guam National Wildlife Refuge. The Navy also manages Orote Ecological Reserve Area which includes land and marine portions on the southern coast of Orote Peninsula. The U.S. National Park Service's War in the Pacific National Historical Park contains three units located entirely in southern Guam. Finally, the Government of Guam has designated Territorial Seashore Park along much of the southwestern coast of the island but the current level of management and protection that the area receives appears to be minimal.