The park consists of two sections, the lowland (closed for visits) and the highland (open for visits). The park is situated in the eastern part of the country, 50 km west of the town of Bukavu, near Lake Kivu and the Rwandan border. It consists of a smaller sector on the eastern side covering part of the Mitumba Mountains, and a larger western sector in the Zairean central basin.
The two zones are connected by a narrow corridor. The entrance to the park is at Tshivanga, on the eastern side. The 75,000 ha eastern sector is entirely montane. The massif is part of the Mitumba Mountain range, the western mountains of the Great Rift Valley. The two main peaks, Mount Kahuzi (3,308 m) and Mount Biéga (2,790 m) are extinct volcanoes, and the massif dates from the late Tertiary or early Quaternary. The lowland sector in the Zairean central basin covers the watersheds of the tributaries of the Luka and Lugulu rivers.
These both drain into the River Lualaba. The extension lies below 1,500 m apart from isolated peaks such as Mount Kamani (1,700 m), and consists of mountains cut by deep valleys. Undulating terrain in the west forms a belt between the two zones. The western zone is forested by equatorial rainforest, with transition forest between 1,200 m and 1,500 m. In the eastern zone, six different primary vegetation types have been distinguished: mountain rainforest, high-altitude rainforest, swamp forest, bamboo forest, subalpine heather and swamp and peat bog.