Nebbi lies between altitudes 2289 ft to 5224 ft above sea level. The landscape offers one of the best sceneries in Uganda. The generally extensive plains of the east gently rise into the undulating hills of the west.

Faulting and rifting along the western arm of the East African rift valley zone extends from the neighboring district of Pakwach from Panyimur into Jukia hills. Up arching and tilting affected the Erussi and Goli uplands. As a result, differences in localized diastrophic forces led to a variation in relief with a marked ascend towards the Democratic Republic of Congo. The district has a raised plateau with metamorphic rocks are. Granitic intrusions on the other hand are a common feature.

The drainage system is basically constituted by Namrwodhu River which has great economic importance with potential sites for electricity generation besides; there are several other minor rivers, springs and wetlands.