About half the Park area is very rugged with steep limestone terrain rising to an altitude of 3,027 m (Mount Binaya), and is hardly explored. This mountainous areas include the Merkele and Kabipoto ridges, other major topographical features are the Manusela valley in the centre of the Park, the northern Wae Mual alluvial plain and the southern Wae Kawa valley.

To the north the Kabipoto ridge descends quite steeply to a coastal plain, which stretches 25 km the North Coast (Wae Mual Plain), in south east the Markele ridge descends steeply into the Taluti bay and in the south west into the narrow Wae Kawa valley.