| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Bandama | River (basin) | native | 103267 |
| Bangweulu | River (basin) | native | 52193 |
| Benue | River (basin) | native | 28663 |
| Buzi | River (basin) | native | 52267 |
| Casamance | River (basin) | native | 33587 |
| Chad | River (basin) | native | 40587 |
| Comoé | River (basin) | native | 81261 |
| Congo | River (basin) | native | 3498 |
| Cross | River (basin) | native | 52861 |
| Ethiopian | Zoogeographic realm | endemic | 40587 |
| Gambia | River (basin) | native | 13331 |
| Incomati | River (basin) | native | 52193 |
| Kainji | Lake | native | 3799 |
| Kariba | Lake | native | 13337 |
| Limpopo | River (basin) | native | 89021 |
| Malawi | Lake | introduced | 55909 |
| Mono | River (basin) | native | 3045 |
| Mweru | Lake | native | 40587 |
| Niger | River (basin) | native | 13331 |
| Nile | River (basin) | questionable | 28714 |
| Ogun | River (basin) | questionable | 3076 |
| Ouémé | River (basin) | native | 13331 |
| Pungwe | River (basin) | native | 13721 |
| Rukwa | Lake | native | 27292 |
| Sabaki | River (basin) | questionable | 30558 |
| Sabi | River (basin) | native | 97235 |
| Senegal | River (basin) | native | 81261 |
| Shire | River (basin) | native | 39192 |
| Tana | River (basin) | questionable | 52331 |
| Upper Lualaba | River (basin) | native | 40587 |
| Volta | River (basin) | native | 13331 |
| Zambezi | River (basin) | native | 40587 |