Most parts of Busia County fall within the Lake Victoria Basin. The altitude is undulating and rises from about 1,130m above sea level at the shores of Lake Victoria to a maximum of about 1,500m in the Samia and North Teso Hills. The central part of the county, especially Butula and Nambale Sub-counties, are occupied by a peneplains marked by low flat divides of approximately uniform height, often capped by lateritic and a shallowly incised swampy drainage system.

The Samia Hills represent the basement complex and consist of acid and sub-acid lavas, tuffs, and agglomerates, banded quartzite and iron stones. The Kavirondo series rocks are developed around Busia, Nambale and Butula while the granites dominate the northern parts of county.

The northern part of the central region features granitic out crops, which is essentially part of the peneplains and is characterized by the presence of large granitic hills and tor such as Amukura and Chelelemuk.

The southern part is covered by a range of hills comprising the Samia and Funyula Hills which run from the north east to the south west culminating at Port Victoria; forming a very conspicuous topographic feature.

The southernmost part of the county is covered by the Yala Swamp which is a down warped area associated with the formation of Lake Victoria. The area forms a colony of papyrus growth and is broken by irregular water channels and occasional small dams with grassy islands. This area is covered with locustrine and alluvial deposits of recent and Pleistocene times.

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