The Köppen climate classification is "Am": equatorial, monsoonal. Temperatures are fairly uniform throughout the year, slightly cooler in July and slightly warmer in April. They range from to, with a mean of just under. Annual rainfall is. Monthly rainfall ranges from in July to in February, with rain falling on about 240 days of each year.
The regions with rich soil have diverse flora and fauna with many endemic species. Mostly the forests are evergreen tropical rainforest on terra firme, not subject to flooding. There is lowland forest along the Amazon River. Further south the forest is submontane, open canopy forest with patches of dense forest. Where the blackwater rivers flood they create igapó forests. An unusual form of forest with many large lianas at all levels is found on the higher land in the south and southeast of the ecoregion. Typically these forests are found on richer soils, and have a canopy under, lower than the canopy of the humid terra firme forest. Lianas belong to the families Bignoniaceae, Fabaceae, Hippocrateaceae, Menispermaceae, Sapindaceae and Malpighiaceae. Large trees in the liana forests include Apuleia molaris, Bagassa guianensis, Caryocar villosum, Hymenaea parvifolia, Tetragastris altissima, Astronium graveolens, Astronium lecointei, Apuleia leiocarpa, Sapium marmieri, Acacia polyphylla, Elizabetha species, Brazil nut and mahogany. Endemic trees and lianas include Cenostigma tocantinum, Ziziphus itacaiunensis and Bauhinia bombaciflora. Common trees in eastern Pará that are not found to the west of the Tapajós include Zollernia paraensi, cupuaçu and Cordia goeldiana. The predominant white-sand igapó forest along the clearwater Tapajós holds species of the family Myrtaceae and trees such as Triplaris surinamensis, Piranhea trifoliata, Copaifera martii, Alchornea castaneifolia and Handroanthus heptaphyllus.
The World Wildlife Fund classes the ecoregion as "Vulnerable". The Tapajós-Xingu, Xingu-Tocantins-Araguaia and Tocantins-Pindara moist forest ecoregions on the eastern edge of the Amazon basin have all been badly affected by human settlement and deforestation. Roads have opened the region to rapid and uncontrolled growth of colonies, logging, ranching and major projects that have destroyed large areas of forest and degraded the land. The remaining forests are threatened by large and uncontrolled man-made fires. Miners seeking gold and other mineral pollute the rivers with chemicals. During the period from 2004 to 2011 the ecoregion experienced an annual rate of habitat loss of 0.38%. Global warming will force tropical species to migrate uphill to find areas with suitable temperature and rainfall. Low, flat, deforested ecoregions such as the Tapajós-Xingu moist forests are extremely vulnerable. The Amazônia National Park protects both sides of the Tapajós near Itaituba, with an area of, but it is underfunded. The Tapajós National Forest does little to protect the forests near Aveiro.