The Katonga River is located in the southwestern part of Uganda.  It is continuous between Lake Victoria and Lake George, reflecting that it once drained away from Lake Victoria into Lake George along its entire length. Regional uplifting events between the two Lakes associated with the western limb (Albertine rift) of the geologically active east African rift system, has caused the swampy region to the south west of Lake wamala to become the new water shade for the Katonga River, which now principally flows east into Lake Victoria, augmented by several tributaries along its course.

During wet seasons, raised water levels in the vicinity of its swampy watershed will occasionally force some water to flow west from this point into the western section of the Katonga River which feeds Lake George, but the bulk of the flow still continues eastwards into Lake Victoria. West of its watershed, the Katonga River is also fed by several tributaries along its course to Lake George.