The exuberant beauty and productivity of nature in Jardines de la Reina make possible a large number of activities where development and conservation will run together as long as a sustainable way of exploitation is observed. Commercial and sports fishing, diving,ecotourism and scientific tourism may coexist if they are properly planned. In Jardines de la Reina are five terrestrial plant formations. Among them, mangroves are predominant with coverage of nearly 80 % of the area. In this forest, red mangrove prevails. This species is fundamental in the productivity of the ecosystems. There are also important coastal xeromorphic plant complexes on sandy and rocky coast, where Coccothrinax littoralis, Metopium toxiferum, Sesuvium portulacastrum and Groton lucidus, are the most abundant. The flora of Jardines de la Reina comprises 66 species of vascular plants from 64 genera and 35 families. The keys with more species are Grande, Caballones and Anclitas.

Insects are the most abundant terrestrial invertebrates with 242 species from 111 families, although spiders, mollusks and chilopods are also present. In spite of the few collections practiced in the area, new species (even for science) have been reported. His fact shows the uniqueness of the fauna of invertebrates of these keys and the potentials to find a lot more as investigations go on. On the other hand, 82 species of birds, 14 species of reptiles and 2 species of mammals, many of which had not been reported for Jardines de la Reina before the 1990s, represent terrestrial vertebrates.
The large number of endemic subspecies suggests that, due to geographic isolation, Jardines de la Reina behaves as an ecological island, where the process of speciation is more intense than in other parts of the Cuban archipelago.

Marine flora comprises 180 species, red algae (72), and green algae (71) are predominant. Besides, 4 species of seagrass are present too. These species of algae and seagrass make up five assemblages: Seagrass (turtle grass) assemblages are the largest and most important regarding marine productivity (picture 13). In the reef lagoon, are turtle grass-manatee grass and turtle grass- brush algae (Penicillus). Up to a depth of 4 m, turtle grass- Halimeda can be found. In the rocky substrate, including the coral reefs, encrusting fan-leaf alga (Lobophora)-sargassum  and y-twig alga (Amphiroa) – pink segmented alga (Jania) assemblages are present.

Marine invertebrates are represented by 5 phyla, 8 classes, 20 orders, 61 families and 165 species. The greatest species richness is that of sponges (60) (picture 16), jellyfish and corals (60), gorgonians (38) (picture 18), crustaceans (pictures 19 and 20), sea urchins and mollusks that are found in almost every marine habitat, most mostly in the complex and beautiful coral reefs.

The predominant marine habitats in Jardines de la Reina are deep and shallow fore reefs, flat rocky bottoms with varying hydrodynamics, reef crests and lagoons.
Fish, reptiles  and mammals represent marine vertebrates. Around 200 fish species are present in the different marine ecosystems. Particularly the fish fauna of the reefs of Jardines de la Reina, ranks first in Cuba regarding richness, density and size, with almost twice more biomass and density than any other Cuban subarchipelago and three times more than any other Caribbean island. The abundance of large and calm snappers and groupers, including jewfish make diving spectacular in the reefs of Jardines de la Reina.

The harmless whale shark , the largest of all sharks, can be seasonably found in the area. This, of course, means an additional and special attraction. Cuba’s four species of sea turtles (loggerheads, hawksbills, leatherbacks and green turtles) can be observed in the beaches and waters of these keys, some of them (green turtles and hawksbills) rather often. Watching a turtle laying eggs at the beach is an unforgettable experience. Cetaceans in the area are a challenge to knowledge, but according to dwellers’ stories, they are more abundant than expected.
Temperature of marine waters always ranges from 24 to 300 C, salinity 36 ‰, and levels of transparency over 40 m during the high tide almost all year long. The level of oxygen and nutrients are excellent for bathing and fishing waters.

During the winter season, the weather is influenced by high-pressure systems coming from the continent (North America) related to cold fronts, while in the summertime, the Azores-Bermudas anticyclone influences the weather. The air temperature ranges from 26 to 310 C during almost the whole year. Under the influence of cold fronts it varies from 24 to 280 C. Humidity varies 85 to 90 % in the summer time and from 70 to 75 % in winter. Winds from the southeast are prevailing. Cloudiness increases gradually during daytime. The sea is usually going from wavy to choppy.

From the geological viewpoint, Jardines de la Reina is a relatively new formation (Pleistocene – Holocene). The keys are highly sensitive to coastal dynamics processes because they are all less than 2 m above sea level and 95 % of their territory is made up of cohesionless sediments. This also makes Jardines de la Reina extremely susceptible to catastrophic damages from severe meteorological events or bad management and development practices. Furthermore, the beaches of the area, lack the quality required to exclusively develop sun and beach tourism, although they are good enough to spend some time enjoying their waters and sands.