[4] The park has a large variety of biological diversity due to the existence within the reserve of eleven different habitats, including rainforest, mangrove forests, swamps, beaches, and lagoons.

[3][4][5] The park, a protected area within the northeastern Caribbean wetlands, was recognized under Ramsar Convention on 3 March 1991 for its rich biological diversity and ecosystems that support threatened flora and fauna species.

Set in a natural wetland of the Caribbean coast, it forms a corridor with another protected area, the Indio Maíz Biological Reserve of Nicaragua.

The depressions are subject to filling by ephemeral floods; estuary lakes, grassy marshes, and wooded swamps caused by very heavy rainfall.

[6] The park has worked with the neighboring village of Tortuguero to help its inhabitants understand that preserving their natural resources is the key to encourage eco-tourism.

There are a large number of interlinked canals, waterways, navigable lagoons, and lakes that create plains of sediment carried by the river system.

[9] The park's wildlife consists of birds, mammals, fungi, ferns, marine life, sea turtles, lakes and rainforest.

Threatened animals species in the reserve area are: the American crocodile (Crocodylus acutus), Baird's tapir (Tapirus bairdii), marine turtles such as Chelonia mydas and Dermochelys coriacea, the manatee or sea cow (Trichechus manatus) (the northeastern Caribbean wetland is its local feeding and reproduction area) and the tropical gar (Atractosteus tropicus) a living fossil brought under protection by Costa Rican legislation.

[4][6][11] Other mammals include three-toed sloths (Bradypus variegatus),[4][6][11] paca (Agouti paca), peccary (Tayassu pecari), tapir (Tapirus bairdii), white-tailed deer (Odocoileus virginianus), armadillo (Dasypus novemcinctus)[5] and [11] 442 species of birds inhabit the area, including kingfishers, toucans, great blue herons and parrots.

[11] Other species include eel,[4] the bull shark (Carcharinus leucas),[4][11] tarpon (Megalops atlanticus), snook (Centropomus parallelus)[11] and tropical gar (Atractosteus tropicus).

[4] Reptiles and amphibians reported are: Caiman crocodilus, Crocodylus acutus, basilisk lizards,[4][6] Chrysemys spp., Rhinoclemmys spp.,[6] poison-dart frogs (Dendrobatidae),[4][6] and many endemic species of salamanders.

There are trees including Dipteryx oleifera, Protium spp., Vatairea spp., Inga spp., Pterocarpus officinalis, Pachira aquatica, Luehea seemannii and Pentaclethra macroloba, with thick and varied undergrowth, and several species of small palms such as Euterpe precatoria.

[6] Trees native to the forests upland to the southwest are Apeiba tibourbou, Astronium graveolens, Brosimum alicastrum, Carapa guianensis, Cordia alliodora, Crescentia cujete, Croton niveus, Dipterix oleifera, Ficus insipida, Hura crepitans, Hymenolobium mesoamericanum, Jacaratia spinosa, Lecointea amazonica, Manilkara zapota, Spondias mombin, Virola sebifera and Zigia longifolia.

[11] Tortuguero National Park is surrounded by private property consisting of large areas under cattle ranching and agricultural farming.

Regulated guidance to visitors to access creeks, lakes, nature trails and watching wildlife and also for observing egg-laying by the turtles Chelonia mydas and Dermochelys coriacea.

[3] Illegal clear-cuts within the park have created access for poachers to the once isolated second-largest green sea turtle nesting beach in the world.

The last named threat is most serious and the most affected species are: Agouti paca, Tayassu pecari, Tapirus bairdii, Odocoileus virginianus, Dasypus novemcinctus and marine turtles and their eggs.