Refuge Cay forms one of the few completely isolated mangrove islands in the Port Royal Mangroves of Kingston Harbour. Consequently, it is home to numerous species of birds which roost and nest in the canopy of the mangrove trees, and also provides a nursery area and feeding ground for aquatic organisms (snapper, snook, jack, shrimp, oysters and lobsters). Refuge cay also forms the north-western border of Hurricane Refuge Lagoon which has provided safe anchorage for large vessels during hurricanes.

Refuge Cay is heavily impacted by solid waste, especially on its north shore, which faces the Kingston Harbour. This has caused the mangrove forest to die in the centre of the cay as the forest is cut off from regular water flow by the build-up of debris. The loss of the mangrove forest cover will see eventual loss of the entire cay and its associated ecological and economic value. An immediate intervention for the rehabilitation of Refuge Cay has been designed which involves removal the solid waste so the free-flow of water is restored and to install solid waste barriers to prevent re-deposition.

The planned intervention to achieve effective rehabilitation may require replanting of seedlings in the cleaned areas of the cay. Work around Refuge Cay began in July, 2017 and the James Moss Solomon Senior Chair and the Centre for Marine Sciences, UWI received a grant from the Kingston Freeport Terminal Limited (KFTL) to carry out the rehabilitation activities.

To date, with the assistance of 23 fishers from Port Royal, a total of over 8200 bags of garbage have been removed from Refuge Cay.