[6] The Zapata Swamp is also a particular habitat of the bee hummingbird, the smallest bird species on the planet.

Zapata is also known for the local endemic Cuban crocodile (Crocodylus rhombifer) which are restricted to the Zapata Swamp and are being reintroduced to the nearby Lanier Swamp on the Isle of Youth (Spanish: Isla de la Juventud).

[3][5][13] The sympatric American crocodile (Crocodylus acutus) also occurs within the Zapata Swamp, and hybridisation between the two species takes place, confirmed by the existence of a Cuban-American hybrid which was found on the Yucatán Peninsula in Mexico after migrating from the swamp.

[14] Within the Zapata Swamp are numerous areas designated for environmental preservation, such as Zapata Swamp Natural Reserve and Las Salinas wildlife sanctuary, which is part of the larger Ciénaga de Zapata Biosphere Reserve (IUCN category VI) which in total is over 6,000 km2 and the largest protected area, not only in Cuba, but also the Caribbean.

Between November and April, the coldest season of the year, the temperature on average is 20 °C (68 °F).