Ospreys, mangrove warblers, and white-crowned pigeons are among the caye's regular inhabitants. Loggerhead turtles and hawksbill turtles, both listed as internationally endangered species, come ashore to lay their eggs on the sandy southern beaches. The hawksbill is exploited for its shell from which ornaments, jewelry and other items are made. Both the loggerhead and the hawksbill are still sought for their meat. The orange flowered Ziricote is the dominant plant species on the western end of the caye, with the red barked Gumbo Limbo and fig trees intermingled throughout.
Coconut palms dominate the eastern end of the caye.
The beautiful spider lily can be found throughout the caye. The waters surrounding Half Moon Caye are teeming with marine life. The shallow lagoon behind the caye is dominated by seagrass beds and interspersed with patch reef and shallow low relief reefs. But it is the reefs to the south and west of the caye which make Lighthouse Reef and Half Moon Caye one of the premiere diving and snorkeling locations in all of Belize. Large schools of fish and gracefull eagle rays continually prowl this part of the park.