| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 106290 |
| Benue | River (basin) | native | 13331 |
| Chad | River (basin) | native | 2917 |
| Congo | River (basin) | native | 7431 |
| Ethiopian | Zoogeographic realm | endemic | 2917 |
| Itimbiri | River (basin) | native | 106290 |
| Kasai | River (basin) | native | 7431 |
| Léfini-Likouala | River (basin) | native | 44840 |
| Lindi-Tshopo | River (basin) | native | 106290 |
| Lualaba | River (basin) | native | 51906 |
| Lukenie | River (basin) | native | 127185 |
| Mai-Ndombe | Lake | native | 1879 |
| Marine Lower Congo | River (basin) | native | 41594 |
| Middle Congo | River (basin) | native | 4910 |
| Niger | River (basin) | native | 2917 |
| Nile | River (basin) | native | 2917 |
| Ogun | River (basin) | native | 13331 |
| Ouémé | River (basin) | native | 13331 |
| Pool Malebo | Lake | native | 41585 |
| Ruki | River (basin) | native | 93897 |
| Sanaga | River (basin) | native | 51193 |
| Sangha | River (basin) | native | 44840 |
| Sankuru | River (basin) | native | 13455 |
| Sewa | River (basin) | native | 13331 |
| Tumba | Lake | native | 41580 |
| Ubangui | River (basin) | native | 45441 |
| Wagenia Falls | River (basin) | native | 106245 |
| White Nile | River (basin) | native | 28714 |