| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 106290 |
| Bangweulu | River (basin) | native | 246 |
| Benue | River (basin) | native | 13331 |
| Chad | River (basin) | native | 2915 |
| Congo | River (basin) | native | 83752 |
| Ethiopian | Zoogeographic realm | endemic | 3203 |
| Itimbiri | River (basin) | native | 106290 |
| Kainji | Lake | native | 3799 |
| Kasai | River (basin) | native | 83752 |
| Lindi-Tshopo | River (basin) | native | 106290 |
| Lower Congo | River (basin) | native | 42510 |
| Lualaba | River (basin) | native | 45616 |
| Marine Lower Congo | River (basin) | native | 1879 |
| Middle Congo | River (basin) | native | 83752 |
| Mweru | Lake | native | 2266 |
| Niger | River (basin) | native | 13331 |
| Ogun | River (basin) | native | 13331 |
| Pool Malebo | Lake | native | 83752 |
| Ruki | River (basin) | native | 93897 |
| Sanaga | River (basin) | questionable | 42510 |
| Sangha | River (basin) | native | 46233 |
| Ubangui | River (basin) | native | 83752 |
| Uélé | River (basin) | native | 83752 |
| Upper Lualaba | River (basin) | native | 45616 |
| Volta | River (basin) | native | 2915 |
| Wagenia Falls | River (basin) | native | 106245 |