| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Ethiopian | Zoogeographic realm | endemic | 7374 |
| Agnébi | River (basin) | native | 13331 |
| Bandama | River (basin) | native | 57290 |
| Benue River | River (basin) | native | 57290 |
| Bia | River (basin) | native | 57290 |
| Boubo | River (basin) | native | 57290 |
| Casamance | River (basin) | native | 57290 |
| Chari-Logone System | River (basin) | native | 57290 |
| Comoé | River (basin) | native | 13331 |
| Congo | River (basin) | native | 93897 |
| Corubal | River (basin) | native | 57290 |
| Cross | River (basin) | native | 57290 |
| Gambia | River (basin) | native | 57290 |
| Great Scarcies | River (basin) | native | 13331 |
| Inner Niger Delta | River (basin) | native | 57290 |
| Itimbiri River | River (basin) | native | 106290 |
| Kasai River | River (basin) | native | 111328 |
| Kogon | River (basin) | native | 57290 |
| Komadugu Yobe | River (basin) | native | 57290 |
| Kwa-Ibo | River (basin) | native | 57290 |
| Léfini-Likouala Region | River (basin) | native | 111328 |
| Lindi-Tshopo Region | River (basin) | native | 106290 |
| Lower Niger | River (basin) | native | 57290 |
| Marine Lower Congo | River (basin) | native | 111328 |
| Middle Congo | River (basin) | native | 111328 |
| Middle Niger | River (basin) | native | 57290 |
| Mono | River (basin) | native | 57290 |
| Niger | River (basin) | native | 57290 |
| Niger Delta | River (basin) | native | 57290 |
| Nile | River (basin) | native | 3575 |
| Ogowe | River (basin) | questionable | 51193 |
| Ogun | River (basin) | native | 57290 |
| Osse | River (basin) | native | 57290 |
| Ouémé | River (basin) | native | 57290 |
| Pampana | River (basin) | native | 57290 |
| Pra | River (basin) | native | 57290 |
| Ruki River Region | River (basin) | native | 93897 |
| San Pedro | River (basin) | native | 57290 |
| Sanaga | River (basin) | native | 51193 |
| Sangha | River (basin) | native | 44840 |
| Sankuru | River (basin) | native | 13455 |
| Sassandra | River (basin) | native | 13331 |
| Senegal | River (basin) | native | 57290 |
| Sewa | River (basin) | native | 57290 |
| Sio | River (basin) | native | 57290 |
| Sokoto | River (basin) | native | 57290 |
| Tano | River (basin) | native | 13331 |
| Ubangui | River (basin) | native | 111328 |
| Uélé | River (basin) | native | 41594 |
| Upper Lualaba | River (basin) | native | 45434 |
| Upper Niger | River (basin) | native | 57290 |
| Wagenia Falls | River (basin) | native | 106245 |
| Kainji Lake | Lake | native | 57290 |
| Malebo Pool | Lake | native | 111328 |
| Tumba | Lake | native | 41580 |
| Ébrié Lagoon | Lagoon | native | 57290 |