| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Albert | Lake | native | 4903 |
| Benue | River (basin) | native | 3064 |
| Black Volta | River (basin) | native | 57125 |
| Blue Nile | River (basin) | native | 28714 |
| Chad | River (basin) | native | 57125 |
| Chari-Logone | River (basin) | native | 331 |
| Cross | River (basin) | native | 81641 |
| Edward | Lake | native | 4903 |
| Ethiopian | Zoogeographic realm | endemic | 3236 |
| Inner Niger Delta | River (basin) | native | 57125 |
| Kainji | Lake | native | 28265 |
| Malagarazi | River (basin) | native | 54847 |
| Middle Niger | River (basin) | native | 57125 |
| Middle Nile | River (basin) | native | 28714 |
| Mono | River (basin) | native | 81641 |
| Niger | River (basin) | native | 3236 |
| Niger Delta | River (basin) | native | 57125 |
| Nile | River (basin) | native | 28714 |
| Ogun | River (basin) | native | 13331 |
| Oti | River (basin) | native | 57125 |
| Ouémé | River (basin) | native | 57125 |
| Rusizi | River (basin) | native | 98755 |
| Sabaki | River (basin) | native | 4904 |
| Sanaga | River (basin) | native | 81639 |
| Senegal | River (basin) | native | 3236 |
| Sokoto | River (basin) | native | 41503 |
| Tana | River (basin) | native | 4909 |
| Tanganyika | Lake | native | 4967 |
| Turkana | Lake | native | 52331 |
| Upper Niger | River (basin) | native | 57125 |
| Victoria | Lake | native | 34290 |
| Victoria Nile | River (basin) | native | 4903 |
| Volta | River (basin) | native | 3236 |
| White Nile | River (basin) | native | 120561 |