Inside, there are healthy habitats for the recovery and refuge of endangered populations of species such as the river wolf (Pteronura brasiliensis), the otter (Lontra longicaudis) and felines such as the yaguarundi (Herpailurus yagouaroundi), the puma (Puma concolor), the jaguar (Panthera onca), the ocelot or tigrillo (Leopardus pardalis) and the margay (Leopardus wiedii).

Among the primate species are the maquisapa (Ateles chamek), the pichico (Saguinus fuscicollis), the emperor pichico (Saguinus imperator), the monkey preserve (Alouatta seniculus), the black-headed monkey (Aotus nigriceps), the woolly monkey (Lagothrix) lagotricha), the friar (Saimiri boliviensis), the squirrel monkey (Saimiri sciureus), the white capuchin (Cebus albifrons) and the black capuchin (Cebus apella).

Other species of mammals that stand out among the wild fauna are the sachavaca (Tapirus terrestris), the huangana (Tayassu pecari), the sajino (Tayassu tajacu), the red deer (Mazama americana), the gray deer (Mazama gouazoubira) and the sloths of two fingers (Choloepus hoffmanni) and three (Bradypus variegatus).

As for the birds, the presence of the harpy eagle (Harpia harpyja), the crested eagle (Morphus guianensis), the common paujil (Mitu tuberosa), the unicorn paujil (Pauxi unicornis) and the carunculado paujil (Crax globulosa) stand out. In the RNTMB, almost all of the macaw species that inhabit Peru are found.

The reptiles are represented mainly by the emerald boa (Corallus caninus), the machaco parrot (Bothrops bilineatus), the boa constrictor (Boa constrictor) and the shushupe (Lachesis muta). It is also common to observe the black alligator (Melanosuchus niger), the white alligator (Caiman crocodylus) and the taricaya (Podocnemis unifilis).

The fish also present a great variety, among them the boquichico (Prochilodus nigricans), the bulging zangaro (Brachyplatystoma filamentosum), the yahuarachi (Potamorrhyna latior), the golden (Brachyplatystoma flavicans) and the paco (Piaractus brachipomun). Among the non-commercial fish are shad (Brycon spp.), Mullet (Schizodon fasciatus) and catfish (Pimelodus sp.).

In the RNTMB there are different types of vegetation, among the main plant associations are the aguajales in the sedimentation plains, the pacales, the terraced forests and the gallery forests. It has identified 17 plant associations by forest type and a total of 1,255 plant species.

A very important species that is conserved in the RNTMB is chestnut (Bertholletia excelsa), which grows in non-flooding terraces of the Amazon lowland forest. In Peru it is located exclusively in the eastern fringe of the department of Madre de Dios and is the most important commercial non-timber species, with great impact on the local economy. It forms a valuable part of the habitat of numerous mammal species because it is a source of food, as well as a shelter for the nesting of raptors.