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 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. Jonam County has a flat relief and Padyere is a raised plateau metamorphic rocks are widespread and sedimentary rocks dominate most parts of Jonam County along Lake Albert Nile basin. Granitic intrusions on the other hand are a common feature in Padyere County.
The drainage system is basically constituted by the Albert Lake and Nile River which are of major economic value to Nebbi. Other river of economic importance is Namrwodhu which contain potential sites for electricity generation besides; there are several other minor rivers, springs and wetlands.