The geology in the Mt. Elgon region comprises of mainly Pre-Cambrian and Cainozoic rock formations including volcanices, granitites, and sediments. The rocks on the slopes are deeply weathered; the dominant soils are Vertisols, regionally known as “black cotton soils”. The top of the mountain are characterized by scarps of agglomerates in linear pattern. The relief is relatively undulating and hilly with the highest catchment elevation at 3,616 m a.s.l. and the lowest at 1,083 m a.s.l.

The catchment is highly influenced by past volcanic activities and the soil is very variable. The impermeable nature of most of the rocks makes the adjacent areas of Mt. Elgon vulnerable to landslides during wet seasons. Topsoils are shallow especially around the Mt. Elgon National Park. Generally, the soils in the highlands are clays, while those in the midlands and the lowlands are clay loams or sandy.