This is a list of freshwater ecoregions in Africa and Madagascar as identified by the World Wildlife Fund (WWF). The WWF categorizes the Earth's land surface into ecoregions, which are defined as "large area[s] of land or water containing a distinct assemblage of natural communities and species." These ecoregions are further grouped into bioregions, "a complex of ecoregions that share a similar biogeographic history, and thus often have strong affinities at higher taxonomic levels (e.g. genera, families)." The Earth's land surface is divided into eight biogeographic realms. While most of Africa falls within the Afrotropical realm, the freshwater ecoregions of North Africa share similarities with the Palearctic realm. Each ecoregion is also classified into major habitat types or biomes. Many view this classification as decisive, and some propose using these boundaries as stable borders for bioregional democracy initiatives.

by Bioregion

North African

Nilo-Sudan

Upper Guinea

West Coast Equatorial

Congo

Great Lakes

Eastern and Coastal

Cuanza

Zambezi

Madagascar and the Indian Ocean Islands

Southern Temperate

by Major Habitat type

Closed basins and small lakes

Floodplains, swamps, and lakes

Moist forest rivers

Mediterranean systems

Highland and mountain systems

Island rivers and lakes

Large lakes

Large river deltas

Large river rapids

Savanna-dry forest rivers

Subterranean and spring systems

Xeric systems