The park consists of the two major valley systems of the Kidepo and Narus Rivers. The valley floors lie between 910 m and 1,200 m above sea level.
Kanangarok is a tepid hot spring in the extreme north of the Park, beside the South Sudanese boundary. This spring is the most permanent source of water in the park. The park predominantly has clay soils although in the Kidepo Valley, black chalky clay and sandy-clay loam predominate, while the Narus Valley has freer-draining red clays and loams.
Kidepo Valley National Park’s climate is divided into one short wet season and a long dry spell. The wet season falls between April and October and the dry season fills the remainder of the year. On average 800 mm of rain is received annually. The dry season is characterised and dominated by very hot north-easterly monsoon winds which results in extreme drought with no green vegetation. At this point temperatures can reach over 40 degrees Celsius and average 30 degrees Celsius. Water is primarily a temporary phenomenon, flowing only during the wet season. However, throughout the length of the Narus River Valley, surface water flow alternates to subterranean flow and emerges at few permanent water points throughout the year. The climate can be summarised as arid but changes to semi arid towards the Narus Valley, which is the only region of the park containing water during the dry season.
The relief of the park rises dramatically from 900-1200m above sea level. on the border with Sudan, to 2750m above sea levell. at the top of the forested mountains of Morungole and Zulia. It comprises of semi-arid plains intersected with hills, rocky out crops and mountain ranges. Two great valley systems divide the park into almost two equal parts. The Narus Valley in the south and west of the park occupies one third of the park and is much favoured by wildlife due to the permanent availability of water. The Kidepo valley system in the east and north-east occupies the remaining two thirds of the entire park. Nyangea-Napore hills and Morungole and Zulia hill ranges hold the sources of most rivers in Karamoja, including River Nalakas and River Kidepo.