The Tapajos APA sprawls across 1,988,445 hectares, divided between the municipalities of Itaituba (85.61%), Jacareacanga (14.12%), and Trairao (0.27%). The Transgarimpeira Road cuts through it from east to west, providing the easiest access and, historically, the easiest route for illegal extraction. The terrain is hilly, deeply eroded, and punctuated by inselbergs, isolated rock formations that rise abruptly from the forest like geological sentinels. Altitudes range from 36 meters in the river valleys to considerably higher on the plateau surfaces. Four major rivers thread through the APA: the Tapajos itself, the Jamanxim, the Crepori, and the Novo. All belong to the Jamanxim sub-basin of the greater Tapajos watershed, a system that drains a vast swath of southern Para.

When Brazil cracked down on illegal logging in and around Novo Progresso in the mid-2000s, the economic consequences were immediate. Logging had been the backbone of the local economy, and enforcement left a vacuum that bred social tension. The government's response was the Tapajos APA, created by federal decree on 13 February 2006. Unlike a national park, an environmental protection area under Brazilian law permits human habitation and economic activity within its bounds, provided they are sustainable. The idea was to open legal timber concessions that would absorb the workforce that enforcement had displaced. ICMBio, the Chico Mendes Institute for Biodiversity Conservation, administers the APA, and a consultative council was established in December 2011 to develop a management plan. The classification is IUCN Category V, a protected landscape that explicitly balances conservation with human use.

Since its creation, the Tapajos APA has been resized repeatedly. In January 2012, Provisional Measure 558 redrew its boundaries along with those of several neighboring parks and forests. About 19,915 hectares were excised to accommodate the planned Jatoba Hydroelectric Power Plant on the Tapajos River, reducing the APA from 2,059,496 hectares by roughly 1%. Law 12678 confirmed the change in June 2012. Then in December 2016, Provisional Measure 758 altered the boundaries again, this time to carve out corridors for the EF-170 railway and the BR-163 highway. Two polygons totaling 862 hectares were removed, while 51,135 hectares were transferred to the adjacent Jamanxim National Park. The net effect shrank the APA further, though the national park gained ground. Each reduction was individually small, each justified by specific infrastructure needs, and each established the principle that protected areas could be trimmed when development demanded it.

For all the political turbulence at its borders, the forest within the Tapajos APA remains remarkably intact. Dense rainforest covers 74% of the area, open rainforest another 24%, and the remaining 2% is a contact zone between cerrado and forest. Altogether, nearly 93% is rainforest, harboring 213 tree species, 2 species of lianas, and 8 palm species. Andiroba and Brazil nut are the most common trees, both economically valuable and ecologically important. The average annual rainfall of 2,250 millimeters sustains a wet, hot climate with temperatures averaging 27 degrees Celsius. The soils are mostly red-yellow acrisols, weathered and nutrient-poor, the kind of ground that supports towering forest only because the ecosystem recycles its own nutrients with brutal efficiency. Remove the trees and the soil bakes to brick within a few seasons. The forest is not just growing on this ground; it is creating the conditions for its own survival.