Permanent streams do not exist in northern or central Chad. Following infrequent rains in the Ennedi Plateau and Ouaddaï Highlands, water may flow through depressions called enneris and wadis. Often the result of flash floods, such streams usually dry out within a few days as the remaining puddles seep into the sandy clay soil. The most important of these streams is the Batha, which in the rainy season carries water west from the Ouaddaï Highlands and the Guéra Massif to Lake Fitri.

Chad's major rivers are the Chari and the Logone and their tributaries, which flow from the southeast into Lake Chad. Both river systems rise in the highlands of Central African Republic and Cameroon, regions that receive more than 1,250 millimeters of rainfall annually. Fed by rivers of Central African Republic, as well as by the Bahr Salamat, Bahr Aouk, and Bahr Sara rivers of southeastern Chad, the Chari River is about 1,200 kilometers long. From its origins near the city of Sarh, the middle course of the Chari makes its way through swampy terrain; the lower Chari is joined by the Logone River near N'Djamena. The Chari's volume varies greatly, from 17 cubic meters per second during the dry season to 340 cubic meters per second during the wettest part of the year.

The Logone River is formed by tributaries flowing from Cameroon and Central African Republic. Both shorter and smaller in volume than the Chari, it flows northeast for 960 kilometers; its volume ranges from five to eighty-five cubic meters per second. At N'Djamena the Logone empties into the Chari, and the combined rivers flow together for thirty kilometers through a large delta and into Lake Chad. At the end of the rainy season in the fall, the river overflows its banks and creates a huge floodplain in the delta.

The seventh largest lake in the world (and the fourth largest in Africa), Lake Chad is located in the sahelian zone, a region just south of the Sahara Desert. The Chari River contributes 95 percent of Lake Chad's water, an average annual volume of 40 billion cubic meters, 95 percent of which is lost to evaporation. The size of the lake is determined by rains in the southern highlands bordering the basin and by temperatures in the Sahel. Fluctuations in both cause the lake to change dramatically in size, from 9,800 square kilometers in the dry season to 25,500 at the end of the rainy season. Lake Chad also changes greatly in size from one year to another. In 1870 its maximum area was 28,000 square kilometers. The measurement dropped to 12,700 in 1908. In the 1940s and 1950s, the lake remained small, but it grew again to 26,000 square kilometers in 1963. The droughts of the late 1960s, early 1970s, and mid-1980s caused Lake Chad to shrink once again, however. The only other lakes of importance in Chad are Lake Fitri, in Batha Prefecture, and Lake Iro, in the marshy southeast.

Data as of December 1988