Protected natural areas include forests of the Commonwealth of Puerto Rico, nature reserves (both marine and estuarine), and wildlife refuges, among others. These areas are designated in various ways depending on the reason for their delimitation, the conservation mechanism used, the agency or entity that owns the land, and who manages the area.

The forests of the Commonwealth of Puerto Rico are established through proclamations issued by the Governor of Puerto Rico in accordance with the Puerto Rico Forest Act (Act 133, 1975), while wildlife refuges are established by the Secretary of the Puerto Rico Department of Natural and Environmental Resources (DRNA) under the Puerto Rico Wildlife Act (Act 241, 1999) and Regulation No. 6765 (Regulation to Govern the Conservation and Management of Wildlife, Exotic Species, and Hunting in the Commonwealth of Puerto Rico). In contrast, nature reserves are established through various mechanisms (Castro-Prieto et al. case, forthcoming): land acquisition through the Forest Legacy Program, which is administered by the DRNA but where the USDA Forest Service provides funding for land acquisition; mitigation measures in development projects; donations; and conservation easements.

The Planning Board and the Legislative Assembly also have the power to designate areas of high ecological value.

The United States government can also designate and manage protected lands by following one of the following mechanisms: it can designate a national forest under the Forest Management Act of 1897; designate a national estuary research reserve under the Federal Coastal Zone Management Act of 1972; or establish natural wildlife refuges under the National Wildlife Refuge System Act of 1966 and the National Wildlife Refuge System Improvements Act of 1997 (Castro-Prieto et al. in press).

There are protected areas that are managed by private entities such as, for example, Para la Naturaleza, Ciudadanos del Karso, Casa Pueblo and Tropic Ventures.

The National Parks Program—now attached to the DRNA—also manages beaches, parks and vacation centers in natural areas of ecological value with facilities for the enjoyment of the public.

According to the inventory of protected areas developed by the Protected Areas Conservation Action Team (PACAT), last updated in December 2016, Puerto Rico has 159 protected areas that occupy 16% (1,436 km2) of the archipelago's surface area. If we do not include the Restricted Zone of the Karst Special Planning Area, these areas comprise approximately 8% of the archipelago (Castro-Prieto et al., in press).

The San Juan Bay Estuary watershed has fourteen (14) protected natural areas comprising 23.7 km² of its area (10% of the total area of ​​the watershed). The largest protected natural areas are: (from largest to smallest)

•   State Pine Forest (8.9 km2)
•  Ciénaga las Cucharillas Nature Reserve (2.8 km2) 
•   Los Frailes Protected Natural Area (2.7Km2).

The municipalities with the largest extension of protected areas are: (from largest to smallest) Loíza (11.6 km2 or 49% of its total area within the basin), San Juan (6.4 km2 or 27% of its area), Cataño (2.8 km2 or 12%) and Bayamón (1.2 km2 or 5%).