Lake Chad also has wide seasonal fluctuations that depend mostly on its main tributary, the Chari, a river barely 1,000 km long that rises in a sub-humid region of the Central African Republic. The May-June rainy season, upstream from the drainage area, determines how the lake will fill between October and January. The dry season causes considerable evaporation (95% of the losses in the lake's water budget) with the lake finding its lowest level in July-August. Even the lake's natural rhythms are therefore unreliable and, because it is relatively shallow, a difference of a few tens of centimetres of accumulated rainfall can cause several tens of thousands of hectares to be covered or uncovered. In drought conditions, the lake may divide into two or three smaller parts: the northern basin is the first to have its salinity rise before drying up completely, while the southern basin, with a less arid climate and fed directly by the Chari River, suffers slighter fluctuations. The marshy or dried-up parts become covered with vegetation, or are fertilised with alluvia.

This situation has contrasting effects on the local economy. The population living around the lake are of many different origins, some as 'climate refugees' from the encroaching Sahara. The lake's shrinkage is harmful to fishing (reduction in fish resources, changes to the balance of species, boats becoming entangled in the vegetation) but beneficial to the development of crops and grazing on the rich alluvial soil. It is hard to quantify the quantities of water removed across the drainage basin by these new agricultural practices. Irrigation and damming the rivers do not seem to have any great impact on the lake's water budget, except during droughts. A major (and controversial) project is being studied with a view to stabilising the fluctuations of Lake Chad in the future: a long artificial canal to feed water into the lake from the Oubangui, a river in the Congo basin.