The Congo River and its tributaries drain this basin and provide the country with the most extensive network of navigable waterways in Africa. Ten kilometers wide at mid-point of its length, the river carries a volume of water that is second only to the Amazon's. Its flow is unusually regular because it is fed by rivers and streams from both sides of the equator; the complementary alternation of rainy and dry seasons on each side of the equator guarantees a regular supply of water for the main channel. At points where navigation is blocked by rapids and waterfalls, the sudden descent of the river creates a hydroelectric potential greater than that found in any other river system on earth.

Most of Zaire is served by the Congo River system, a fact that has facilitated both trade and outside penetration. Its network of waterways is dense and evenly distributed through the country, with three exceptions: northeastern Mayombé in Bas-Zaïre Region in the west, which is drained by a small coastal river called the Shilango; a strip of land on the eastern border adjoining lakes Edward and Albert, which is part of the Nile River basin; and a small part of extreme southeastern Zaire, which lies in the Zambezi River basin and drains into the Indian Ocean.

Most of Zaire's lakes are also part of the Congo River basin. In the west are Lac Mai-Ndombe and Lac Tumba, which are remnants of a huge interior lake that once occupied the entire basin prior to the breach of the basin's edge by the Congo River and the subsequent drainage of the interior. In the southeast, Lake Mweru straddles the border with Zambia. On the eastern frontier, Lac Kivu, Central Africa's highest lake and a key tourist center, and Lake Tanganyika, just south of Lac Kivu, both feed into the Lualaba River, the name often given to the upper extension of the Congo River. Only the waters of the eastern frontier's northernmost great lakes, Edward and Albert, drain north, into the Nile Basin.