To the north of the Amazon, the mouth of the Rio Apayacu is nearly opposite the mouth of the Rio Orosa, and the Sabalillo Forest Preserve is approximately 40 km upriver. Inhabitants of both areas belong to the Yagua Indian ethnic group, and live in small villages, mostly along the lower reaches of both rivers. The terrain in the 'Bajo Amazonas' region is relatively flat with low rolling hills in areas away from the rivers. Elevation at river level is about 100m above sea level, and the highest elevations are approximately 150m. Vegetation is tropical rainforest with areas of mixed agriculture near communities and patches of secondary forest where orchards and fields have been abandoned.
Soils are highly weathered and nutrient poor.
One prominent geological feature is the widespread and shell-rich Pevas Formation, deposited when the western Amazon region was covered by a huge inland sea. There is considerable environmental heterogeneity, even within small geographic areas, and this heterogeneity is important in maintaining the high biodiversity of the Amazon region in general. A number of distinct habitats are accessible and available for research projects and study at Project Amazonas' field stations. A variety of upland successional habitats and old peach palm and plantain plantations of differing ages are located in the immediate vicinity of the Madre Selva site. At both Madre Selva and Paucarillo, primary forest extends southward unbroken to the Brazilian frontier, some 100 km distant.