Despite its smaller size, it is a highly aggressive animal (one of the most territorial of all crocodilians), and potentially dangerous to humans.

Its preferred habitat comprises freshwater and brackish water environments, such as mangrove swamps, coastal lagoons, estuaries, marshes, floodplains, and river deltas.

Captive animals have displayed cooperative hunting behavior, and can be taught tricks, suggesting intelligence.

Once spread across the Caribbean, its range has dwindled to including only the Zapata Swamp and Isla de la Juventud, due to hunting by humans.

[7] Phylogenetic evidence supports Crocodylus diverging from its closest recent relative (the extinct Voay of Madagascar) around 25 million years ago, near the Oligocene/Miocene boundary.

[6] Below is a cladogram utilizing data from a 2018 tip dating study by Lee & Yates, simultaneously using morphological, molecular (DNA sequencing), and stratigraphic (fossil age) data,[8] as revised by the 2021 Hekkala et al. paleogenomics study using DNA extracted from the extinct Voay.

[12] Today, the Cuban crocodile can only be found in Cuba's Zapata Swamp and Isla de la Juventud, where it is highly endangered.

It formerly ranged elsewhere in the Caribbean; fossils of this species have been found in the Cayman Islands,[13] The Bahamas[14][15] and Hispaniola (the Dominican Republic).

[16] The Cuban crocodile appears to favor freshwater habitat such as swamps, marshes, and rivers and rarely swims in saltwater.

[26] In the wild, crocodiles will nest in wet marshes; where they will create trenches and cover the eggs with organic material.

In conservation, the eggs are kept in incubators that provide a constant environment of 32 degrees Celsius in order to produce males.

The species is represented in captivity in Europe, the United States,[28][29] and in at least one zoo in India,[30][31][32] where breeding projects are taking place.

When Shatalov could no longer take care of the crocodiles, they were given to the Moscow Zoo, which in turn gifted them to the Skansen aquarium in 1981.