[1] The ecoregion is in the Neotropical realm and the tropical and subtropical moist broadleaf forests biome.

There is a wide variety of species in the dense evergreen rainforest due to the many rivers and to the transitional nature of the flora between the Amazon basin and the drier southern vegetation.

Common species in the igapó and várzea include Caraipa grandiflora, Virola surinamensis, Euterpe oleraceae, Ficus pulchella, Mauritia martiana, Symphonia globulifera, and members of the Tovomita and Clusia genera.

[1] The most common families in the terra firme forests are Lecythidaceae, Chrysobalanaceae, Burseraceae, Fabaceae, Lauraceae and Sapotaceae.

The legume Vouacapoua americana is the most important timber tree, growing only in the east of the Amazon region.

Mammals include red-handed howler (Alouatta belzebul), red-handed tamarin (Saguinus midas), brown-throated sloth (Bradypus variegatus), Linnaeus's two-toed sloth (Choloepus didactylus) and nine-banded armadillo (Dasypus novemcinctus).

[1] Endangered mammals include white-cheeked spider monkey (Ateles marginatus), black bearded saki (Chiropotes satanas) and giant otter (Pteronura brasiliensis).

[1] Endangered birds include red-necked aracari (Pteroglossus bitorquatus) and yellow-bellied seedeater (Sporophila nigricollis).

[5] The Tapajós–Xingu, Xingu–Tocantins–Araguaia, and Tocantins–Araguaia–Maranhão moist forests ecoregions on the eastern edge of the Amazon basin have all been badly affected by human settlement and deforestation.

The Tucuruí Dam on the Tocantins below Marabá flooded 2,430 square kilometres (940 sq mi) of low-lying forest.

Seedlings of rainforest trees cannot grow in the dry and eroded pastures, so forest regeneration is difficult.

[7] Global warming will force tropical species to migrate uphill to find areas with suitable temperature and rainfall.

The Caxiuanã National Forest covers 2,000 square kilometres (770 sq mi) and offers a degree of protection.