Uganda is a well-watered country. Nearly one-fifth of the total area, or 44,000 square kilometers, is open water or swampland. Four of East Africa's Great Lakes--Lake Victoria, Lake Kyoga, Lake Albert, and Lake Edward--lie within Uganda or on its borders. Lake Victoria dominates the southeastern corner of the nation, with almost one-half of its 10,200-square-kilometer area lying inside Ugandan territory. It is the second largest inland freshwater lake in the world (after Lake Superior), and it feeds the upper waters of the Nile River, which is referred to in this region as the Victoria Nile.

Lake Kyoga and the surrounding basin dominate central Uganda. Extensions of Lake Kyoga include Lake Kwania, Lake Bugondo, and Lake Opeta. These "finger lakes" are surrounded by swampland during rainy seasons. All lakes in the Lake Kyoga Basin are shallow, usually reaching a depth of only eight or nine meters, and Lake Opeta forms a separate lake during dry seasons. Along the border with Zaire, Lake Albert, Lake Edward, and Lake George occupy troughs in the western Rift Valley.

Leaving Lake Victoria at Owen Falls, the Victoria Nile descends as it travels toward the northwest. Widening to form Lake Kyoga, the Nile receives the Kafu River from the west before flowing north to Lake Albert. From Lake Albert, the Nile is known as the Albert Nile as it travels roughly 200 kilometers to the Sudan border. In southern and western Uganda, geological activity over several centuries has shifted drainage patterns. The land west of Lake Victoria is traversed by valleys that were once rivers carrying the waters of Lake Victoria into the Congo River system. The Katonga River flows westward from Lake Victoria to Lake George. Lake George and Lake Edward are connected by the Kizinga Channel. The Semliki River flows into Lake Edward from the north, where it drains parts of Zaire and forms a portion of the Uganda-Zaire border.

Spectacular waterfalls occur at Murchison (Kabalega) Falls on the Victoria Nile River just east of Lake Albert. At the narrowest point on the falls, the waters of the Nile pass through an opening barely seven meters wide. One of the tributaries of the Albert Nile, the Zoka River, drains the northwestern corner of Uganda, a region still popularly known as the West Nile although that name was not officially recognized in 1989. Other major rivers include the Achwa River (called the Aswa in Sudan) in the north, the Pager River and the Dopeth-Okok River in the northeast, and the Mpologoma River, which drains into Lake Kyoga from the southeast.