[2] The nature reserve is famous for its otherworldly lagoon that contains some of the oldest geologic formations in Puerto Rico, in addition to its beaches, coral reefs, mangroves, dry forests and karst caves, one of which is associated with the pirate and folk figure Roberto Cofresí.

[3] Apart from its ecological value, the nature reserve also contains and preserves important archaeological sites associated with the indigenous Taino cultures and, more recently, Hacienda La Romana, a 19th-century sugarcane plantation.

Dating from the Early Cretaceous, more than 11,000,000 years ago, Punta Guaniquilla also contains some of the oldest geologic formations in Puerto Rico together with the nearby Sierra Bermeja hills.

Key plant species include all three species of mangrove native to Puerto Rico in addition to the almácigo (Bursera simaruba), the coast zapote (Manilkara pleeana), the marunguey (Zamia portoricensis), the pipe organ cactus (Pilosocereus royenii), the Puerto Rico manjack (Varronia rupicola), the roving pricklypear (Opuntia repens), the West Indian mahogany (Swietenia mahagoni), and the rare bromeliad Hohenbergia antillana.

Throughout its history, some of the caves in the peninsula were used for smuggling, to the point that they were locally associated with the folklore surrounding the pirate Roberto Cofresí, who was active in the area during the early 19th century.