| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Benue | River (basin) | native | 13331 |
| Blue Nile | River (basin) | native | 28714 |
| Chad | River (basin) | native | 3203 |
| Ethiopian | Zoogeographic realm | endemic | 3203 |
| Gambia | River (basin) | native | 3203 |
| Géba | River (basin) | native | 13331 |
| Kainji | Lake | native | 3799 |
| Middle Nile | River (basin) | native | 28714 |
| Niger | River (basin) | native | 3203 |
| Nile | River (basin) | native | 28714 |
| Ogun | River (basin) | native | 13331 |
| Ouémé | River (basin) | native | 13331 |
| Senegal | River (basin) | native | 3203 |
| Turkana | Lake | native | 52331 |
| Volta | River (basin) | native | 52865 |
| Volta | River (basin) | native | 3203 |
| White Nile | River (basin) | native | 120561 |