| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agnébi | River (basin) | native | 57129 |
| Ankobra | River (basin) | native | 57129 |
| Aruwimi | River (basin) | native | 106290 |
| Bandama | River (basin) | native | 57129 |
| Bangweulu | River (basin) | native | 52961 |
| Benue | River (basin) | native | 57129 |
| Bia | River (basin) | native | 83625 |
| Buzi | River (basin) | native | 270 |
| Cavally | River (basin) | native | 57129 |
| Chad | River (basin) | native | 57129 |
| Chari-Logone | River (basin) | native | 57129 |
| Comoé | River (basin) | native | 57129 |
| Congo | River (basin) | native | 270 |
| Cross | River (basin) | native | 81644 |
| Ébrié | Lagoon | native | 57129 |
| Eholié | River (basin) | native | 83625 |
| Ethiopian | Zoogeographic realm | endemic | 270 |
| Gambia | River (basin) | native | 57129 |
| Great Scarcies | River (basin) | native | 13331 |
| Itimbiri | River (basin) | native | 106290 |
| Kainji | Lake | native | 57129 |
| Kariba | Lake | native | 270 |
| Kasai | River (basin) | native | 11970 |
| Kogon | River (basin) | native | 57129 |
| Little Scarcies | River (basin) | native | 13331 |
| Lomami | River (basin) | native | 106245 |
| Lower Congo | River (basin) | native | 42510 |
| Lower Zambezi | River (basin) | native | 95585 |
| Lualaba | River (basin) | native | 36901 |
| Mai-Ndombe | Lake | native | 41589 |
| Malagarazi | River (basin) | native | 27292 |
| Malawi | Lake | native | 270 |
| Middle Congo | River (basin) | native | 4910 |
| Middle Nile | River (basin) | native | 28714 |
| Middle Zambezi | River (basin) | native | 95585 |
| Moa | River (basin) | native | 13331 |
| Mono | River (basin) | native | 57129 |
| Mweru | Lake | native | 36901 |
| Niger | River (basin) | native | 57129 |
| Niger Delta | River (basin) | native | 57129 |
| Nile | River (basin) | native | 270 |
| Ogowe | River (basin) | native | 81644 |
| Ogun | River (basin) | native | 57129 |
| Pool Malebo | Lake | native | 36901 |
| Pra | River (basin) | native | 30488 |
| Pungwe | River (basin) | native | 270 |
| Rufiji | River (basin) | native | 27292 |
| Ruki | River (basin) | native | 93897 |
| Rukwa | Lake | questionable | 27292 |
| Saint Paul | River (basin) | native | 13331 |
| San Pedro | River (basin) | native | 13331 |
| Sanaga | River (basin) | native | 81644 |
| Sassandra | River (basin) | native | 57129 |
| Senegal | River (basin) | native | 57129 |
| Sewa | River (basin) | native | 13331 |
| Shire | River (basin) | native | 270 |
| Tanganyika | Lake | native | 7248 |
| Tano | River (basin) | native | 13331 |
| Turkana | Lake | native | 52871 |
| Ubangui | River (basin) | native | 45441 |
| Uélé | River (basin) | native | 270 |
| Upper Lualaba | River (basin) | native | 36901 |
| Upper Niger | River (basin) | native | 57129 |
| Volta | River (basin) | native | 57129 |
| Wagenia Falls | River (basin) | native | 106245 |
| Wami | River (basin) | native | 27292 |
| White Nile | River (basin) | native | 28714 |
| Zambezi | River (basin) | native | 78218 |