| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Benue | River (basin) | native | 57126 |
| Chad | River (basin) | native | 57126 |
| Chari-Logone | River (basin) | native | 96687 |
| Ethiopian | Zoogeographic realm | endemic | 3236 |
| Gambia | River (basin) | native | 96687 |
| Inner Niger Delta | River (basin) | native | 57126 |
| Kainji | Lake | native | 57126 |
| Lower Nile | River (basin) | native | 51850 |
| Middle Niger | River (basin) | native | 51850 |
| Middle Nile | River (basin) | native | 28714 |
| Niger | River (basin) | native | 57126 |
| Nile | River (basin) | native | 28714 |
| Senegal | River (basin) | native | 96687 |
| Turkana | Lake | native | 96687 |
| Volta | River (basin) | questionable | 13331 |
| White Nile | River (basin) | native | 120561 |