| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Benue | River (basin) | native | 57127 |
| Blue Nile | River (basin) | native | 43912 |
| Chad | River (basin) | native | 57127 |
| Chari-Logone | River (basin) | native | 57127 |
| Comoé | River (basin) | native | 57127 |
| Ethiopian | Zoogeographic realm | endemic | 3570 |
| Inner Niger Delta | River (basin) | native | 57127 |
| Kainji | Lake | native | 57127 |
| Komadugu Yobe | River (basin) | native | 57127 |
| Lower Niger | River (basin) | native | 57127 |
| Lower Nile | River (basin) | native | 43912 |
| Middle Niger | River (basin) | native | 57127 |
| Niger | River (basin) | native | 57127 |
| Niger Delta | River (basin) | native | 57127 |
| Nile | River (basin) | native | 28714 |
| Nile Delta | River (basin) | native | 43912 |
| Sokoto | River (basin) | native | 57127 |
| Upper Niger | River (basin) | native | 57127 |
| Volta | River (basin) | native | 57127 |
| White Nile | River (basin) | native | 120561 |