| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agnébi | River (basin) | native | 13331 |
| Aruwimi | River (basin) | native | 106290 |
| Bandama | River (basin) | native | 13331 |
| Benue | River (basin) | native | 13331 |
| Blue Nile | River (basin) | native | 28714 |
| Chad | River (basin) | native | 3203 |
| Comoé | River (basin) | native | 13331 |
| Congo | River (basin) | native | 93897 |
| Ethiopian | Zoogeographic realm | endemic | 3203 |
| Gambia | River (basin) | native | 3203 |
| Itimbiri | River (basin) | native | 106290 |
| Kasai | River (basin) | native | 41591 |
| Lindi-Tshopo | River (basin) | native | 106290 |
| Lualaba | River (basin) | native | 41590 |
| Middle Congo | River (basin) | native | 4910 |
| Middle Nile | River (basin) | native | 28714 |
| Mono | River (basin) | native | 13331 |
| Mweru | Lake | native | 41590 |
| Niger | River (basin) | native | 3203 |
| Nile | River (basin) | native | 28714 |
| Ogun | River (basin) | native | 13331 |
| Ouémé | River (basin) | native | 13331 |
| Pool Malebo | Lake | native | 41585 |
| Ruki | River (basin) | native | 93897 |
| Sassandra | River (basin) | native | 13331 |
| Senegal | River (basin) | native | 2915 |
| Tumba | Lake | native | 41580 |
| Ubangui | River (basin) | native | 42005 |
| Upper Lualaba | River (basin) | native | 2970 |
| Upper Niger | River (basin) | native | 81274 |
| Volta | River (basin) | native | 3203 |
| Wagenia Falls | River (basin) | native | 106245 |
| White Nile | River (basin) | native | 120561 |