The ecoregion is one of the most severely degraded of the Amazon region, suffering from large-scale deforestation and selective extraction of timber, particularly along the Trans-Amazonian Highway and in the higher and more populated southern portions.

The north of the ecoregion is on the lowland Amazon basin, while in the south it rises into the higher ground of the Brazilian Shield.

[2] Elevations range from sea level at the Amazon to 396 metres (1,299 ft) in the Carajás Mountains in the south.

[1] In the south the ecoregion is broken up by areas of savanna woodlands from the cerrado biome of the Central Brazilian Plateau.

There are 8 species of primates including the white-nosed saki (Chiropotes albinasus), red-handed tamarin (Saguinus midas), red-bellied titi (Callicebus moloch), Azara's night monkey (Aotus azarae infulatus) and white-cheeked spider monkey (Ateles marginatus).

Other species of mammals include white-lipped peccary (Tayassu pecari), collared peccary (Dicotyles tajacu), cougar (Puma concolor), jaguar (Panthera onca), South American tapir (Tapirus terrestris), brocket deer (genus Mazama), bare-tailed woolly opossum (Caluromys philander), and seven-banded armadillo (Dasypus septemcinctus).

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

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

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

The remaining forest has been stripped of its valuable trees, and many native fauna and flora have become locally extinct.

Large-scale mining near Marabá and elsewhere have directly affected the environment, and demand large quantities of wood to run the smelters.

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