| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agnébi | River (basin) | native | 81279 |
| Albert | Lake | native | 42019 |
| Aruwimi | River (basin) | native | 42019 |
| Bandama | River (basin) | native | 81279 |
| Benue | River (basin) | native | 81279 |
| Bia | River (basin) | native | 81279 |
| Blue Nile | River (basin) | native | 28714 |
| Boubo | River (basin) | native | 81279 |
| Cavally | River (basin) | native | 81279 |
| Cess | River (basin) | native | 81279 |
| Chad | River (basin) | native | 81279 |
| Chari-Logone | River (basin) | native | 42019 |
| Chiloango | River (basin) | native | 80290 |
| Comoé | River (basin) | native | 81279 |
| Congo | River (basin) | native | 42019 |
| Corubal | River (basin) | native | 81279 |
| Cross | River (basin) | native | 80290 |
| Ébrié | Lagoon | native | 81279 |
| Ethiopian | Zoogeographic realm | endemic | 5331 |
| Fatala | River (basin) | native | 81279 |
| Gambia | River (basin) | questionable | 81279 |
| Géba | River (basin) | native | 13331 |
| Great Scarcies | River (basin) | native | 81279 |
| Itimbiri | River (basin) | native | 42019 |
| Kainji | Lake | native | 28265 |
| Kasai | River (basin) | native | 42019 |
| Kienke | River (basin) | native | 80290 |
| Kogon | River (basin) | native | 81279 |
| Komo | River (basin) | native | 80290 |
| Konkouré | River (basin) | native | 81279 |
| Kouilou-Niari | River (basin) | native | 80290 |
| Kwilu | River (basin) | native | 42019 |
| Léfini-Likouala | River (basin) | native | 44840 |
| Lindi-Tshopo | River (basin) | native | 42019 |
| Little Scarcies | River (basin) | native | 81279 |
| Loémé | River (basin) | native | 80290 |
| Lofa | River (basin) | native | 81279 |
| Lokoundje | River (basin) | native | 80290 |
| Lomami | River (basin) | native | 42019 |
| Lower Congo | River (basin) | native | 42510 |
| Lualaba | River (basin) | native | 5331 |
| Lukenie | River (basin) | native | 42019 |
| Mbini | River (basin) | native | 80290 |
| Middle Congo | River (basin) | native | 41590 |
| Middle Nile | River (basin) | native | 28714 |
| Moa | River (basin) | native | 81279 |
| Mono | River (basin) | native | 81279 |
| Mungo | River (basin) | native | 80290 |
| Mweru | Lake | native | 42019 |
| Niger | River (basin) | native | 81279 |
| Nile | River (basin) | native | 28714 |
| Ntem | River (basin) | native | 80290 |
| Nyanga | River (basin) | native | 80290 |
| Nyong | River (basin) | native | 80290 |
| Ogowe | River (basin) | native | 80290 |
| Ogun | River (basin) | native | 81279 |
| Ouémé | River (basin) | native | 81279 |
| Pampana | River (basin) | native | 81279 |
| Pool Malebo | Lake | native | 42019 |
| Pra | River (basin) | native | 81279 |
| Rokel | River (basin) | native | 81279 |
| Ruki | River (basin) | native | 42019 |
| Saint John | River (basin) | native | 81279 |
| Saint Paul | River (basin) | native | 81279 |
| San Pedro | River (basin) | native | 81279 |
| Sanaga | River (basin) | native | 80290 |
| Sangha | River (basin) | native | 42019 |
| Sassandra | River (basin) | native | 81279 |
| Senegal | River (basin) | native | 81279 |
| Sewa | River (basin) | native | 81279 |
| Tano | River (basin) | native | 13331 |
| Tumba | Lake | native | 41580 |
| Turkana | Lake | native | 28663 |
| Ubangui | River (basin) | native | 42019 |
| Uélé | River (basin) | native | 42019 |
| Upper Lualaba | River (basin) | native | 5331 |
| Victoria | Lake | questionable | 5331 |
| Volta | River (basin) | native | 81279 |
| Wagenia Falls | River (basin) | native | 109245 |
| White Nile | River (basin) | native | 120561 |
| Wouri | River (basin) | native | 80290 |