Lake Chad's size varies greatly depending on the season and time of year. In October, Lake Chad's surface area can exceed 9,950 square miles (28,457 sq. km), but by late April or early May, the area will have decreased to roughly 3,000 square miles (8580 sq. km). Within the lake, one can find many large islands which occasionally join together during droughts or the dry season. The overall volume of the lake is determined by the amount of rainfall that has occurred that year and also by how much water has been lost through evaporation, transpiration through plants and seepage. The Chari (Shari)-Longe River is the main source of water for Lake Chad, accounting for about a fifth of the total volume of water flowing into the lake. The remaining water comes from the Ebeji (El-Béid) and Yedseram Rivers. On average, over 100 inches (2545 mm) of water is consumed by plants or evaporates during the dry season. Researchers believe that at least 10 inches (255 mm) of Lake Chad water flows as ground water to neighboring Manga and Kanem lowlands and as underflow in the El-Ghazal River.

A low ridge that extends from the northeast to the southwest corner of the lake divides Lake Chad into two separate pools. This ridge was formed during a terrible drought in the early 20th century. On some occasions, the ridge will actually cause the two pools to become completely separate bodies of water, however it depends on how the rainfall and evaporation rates balance out. In general, the eastern pool can have a depth of 33 ft (9.9 m) while the northeastern pool is 13 to 23 ft (4.7 - 6.9 m) deep. The southeastern pool tends to be the shallowest - 10 to 13 ft (3 - 3.9 m) deep - because of its sediment feed from the Chari River. However, along the archipelago, the southeastern pool can reach depths of up to 36 ft (10.8 m). Overall, the dry-season winds have a profound effect on the water levels at any given time.

Interestingly enough, Lake Chad has a very low salt content in spite of the fact that it is a dryland lake and does not have any true outlets. However, during the dry season, salt content will increase because of the low levels of rainfall. In general, the northeastern shoreline has the highest levels of salt recorded.

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