The Palisadoes-Port Royal Protected Area (PPRPA), an NRCA designated protected area of approximately 7,523 hectares in size, encompasses both terrestrial and marine areas. Prior to the 1998 NRCA designation, the Palisadoes-Port Royal Protected Area was previously declared in 1967 under the Beach Control Act (BCA). The area includes Jamaica's second Wetland of International Importance (Ramsar Site) declared under the Convention on Wetlands of International Importance, especially as a Waterfowl Habitat on 22 April 2005. The protected area also encompasses the Port Royal and the Palisades Protected National Heritage, designated under the Jamaica National Heritage Trust (JNHT) Act. The Draft Palisadoes-Port Royal Protected Area Zoning Plan, 2014–2019, prepared by the National Environment and Planning Agency, identifies three areas within the Palisadoes-Port Royal Protected Area as conservation sites.

The conservation sites identified by the Draft Plan prepared in 2014 and revised in 2018 are as follows:

• Conservation Zone A: This area encompasses the Buccaneer Swamp (the wetland area immediately to the south and west of lands housing the Royal Jamaica Yacht Club) and includes the entire expanse of mangrove lagoons extending toward the Norman Manley Highway.

• Conservation Zone B: To the north, the area includes the Port Royal mangroves (inclusive of Refuge Cay). To the north, the area includes the Port Royal mangroves (inclusive of Refuge Cay). In addition to its significance as a nursery, this segment of Conservation Zone B is also an important habitat for several species of birds, including the Brown Pelican. The southern boundary of this zone extends from the Plumb Point Lighthouse, ending at a vacant lot adjacent to the Port Royal Basic School, and is marked by the presence of coastal scrub vegetation and dune ecosystems. Conservation Zone B area includes a significant archaeological site Fort Rupert (submerged in the Lagoon) as well as part of the buffer zone in which several historic sites are located.

• Conservation Zone C: This includes the barrier reef system along South and South-East Cay.