There are various types of vegetation growing in the forest, ranging from 170ft (52m) gigantic hardwoods to small saplings that are only a few inches (~10cm) in diameter. Because of the large number of trees growing throughout the forest, the forest floor is a vast network of entangled roots which in some cases makes it impossible to pass through sections of the forest on foot. In many areas, the high canopy is so dense that only small amounts of sunlight peek through the trees and reach the forest floor. Due to the lack of light, the lower levels of the forest have very little vegetation growing, if any at all. Where gaps in the canopy are large enough to allow sunlight to penetrate, large herbaceous plants with long leaves grow in dense groupings. The forest attracts many types of wildlife which feed off the large amounts of fruits and nuts that have fallen to the ground.

The Ituri Forest has many streams and rivers that flow from east to west through the forest. The Ituri River is accompanied by several other rivers such as the Nepoko to the north, the Epulu and Nduye in the central part and the Ibina to the south. The majority of the rivers are not navigable for more than several miles at a time because of the varying density of vegetation. Each year over 75 inches (1,900 mm) of rain falls in the forest and contributes to the streams flowing through the forest. On average, there are 2,000 hours of sunshine per year (roughly 180 days out of the year). The Ituri Forest goes through a dry season in the period December-February, when there is less than 7 inches of rainfall. The heaviest rains occur in October and early November. It is during these months that streams will flood, making it almost impossible to travel long distances in the forest itself. The average temperature is generally 88(F (31(C) year-round. During the dry season small streams dry up and the humidity is greatly reduced.

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