| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Benue River | River (basin) | native | 13331 |
| Chari-Logone System | River (basin) | native | 57125 |
| Ethiopian | Zoogeographic realm | endemic | 27886 |
| Inner Niger Delta | River (basin) | native | 57125 |
| Kainji Lake | Lake | native | 28265 |
| Lake Turkana | Lake | native | 43507 |
| Niger | River (basin) | native | 57125 |
| Nile | River (basin) | native | 3236 |
| Ouémé | River (basin) | native | 57125 |
| Senegal | River (basin) | native | 57125 |