Geological results of the Uganda Museum’s Baker Centenary Expedition stressed the importance of rift control in land-surface development and sedimentation since early Miocene times. The Kisegi-Wasa area north of the fault “nose” of Ruwenzori exposes late Tertiary sediments that grade upward without angular discordance into a thick conformable series of gently dipping lacustrine deposits (Kaiso Series) which yield abundant mollusk and fish fossils but few mammal fossils. The mammals are typical of shallow-water conditions and include species recorded from the lower Villafranchian of North Africa. Higher in the sequence occur forms that range through the upper Villafranchian, whereas the uppermost Kaiso sediments may be mid-Pleistocene. They are overlain unconformably by unfossiliferous later Pleistocene deposits. Morphological mapping reveals an intricate network of late Pleistocene grid faults associated with upthrust of the Ruwenzori block. In sharp contrast with the Kisegi-Wasa area, the Murchison Falls area has experienced a stable Quaternary history. Late grid faults and typical Kaiso deposits are absent. The boundary faults of the graben have been at least partly buried by sediments, and they stand as escarpments only where exhumed by differential erosion. The Murchison Falls itself is the result of retreat from a buried fault line following superposition from a deeply lateritized surface of rift sediments covered by a duricrust. Rise in the level of Lake Albert over the last 4 years is related to the problem of recognizing Pleistocene “pluvial” (and “nonpluvial”) phases. High discharge at Murchison Falls has resulted in a former channel being re-occupied by the Nile, followed by rapid morphological change.