Considered as a wildlife sanctuary with areas of high value of biodiversity conservation. The reserve has the largest tropical lake systems in the country: Cuyabeno and Lagartococha River.

The environment is made of mainland forests, flooded forests, swamps, rivers and lagoons. Tropical forests are known to possess the greatest number of living species. The flora is one of the most diverse on the planet, with more than 12,000 species distributed in different habitats. There are about 1,320 species: 165 mammals, 493 birds, 96 amphibians, 91 reptiles and 475 kinds of fishes. There are 493 species of birds ; 31 are rare, 3 are very rare: common seagull, tui parakeet and violet partridge pigeon.

are a big variety of mammals living in these forests: tigrillos, mate’s head, dantas, armadillos, collar peccary, peccaries, anteaters, water foxes, woolly raposas.
Cuyabeno is home of 10 kinds of primates. Among the most representatives  we can mention the leoncillo or also known as pocket monkey, the smallest in the world, the black or yellow-walled, a new record for the fauna of Ecuador. They are also found: chorongos, howler monkeys, varicose veins that are associated in groups of up to 100 individuals.
Also exist acuatic mammals like the pink dolphin, giant otter and manatee. The Lagartococha lake complex is the only site in Ecuador where manatee populations can still be observed.