| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Abaya | Lake | native | 58460 |
| Bandama | River (basin) | native | 81285 |
| Bani | River (basin) | native | 81285 |
| Benue River | River (basin) | native | 81285 |
| Boubo | River (basin) | native | 45853 |
| Chari-Logone System | River (basin) | native | 81285 |
| Comoé | River (basin) | native | 81285 |
| Congo | River (basin) | native | 3636 |
| Corubal | River (basin) | native | 13331 |
| Cross | River (basin) | native | 13331 |
| Ethiopian | Zoogeographic realm | endemic | 2756 |
| Fatala | River (basin) | native | 81285 |
| Gambia | River (basin) | questionable | 3074 |
| Géba | River (basin) | native | 13331 |
| Great Scarcies | River (basin) | native | 13331 |
| Inner Niger Delta | River (basin) | native | 81285 |
| Kainji Lake | Lake | native | 28265 |
| Kasai River | River (basin) | native | 2970 |
| Kogon | River (basin) | native | 81285 |
| Komadugu Yobe | River (basin) | native | 81285 |
| Konkouré | River (basin) | native | 81285 |
| Lake Turkana | Lake | native | 52331 |
| Lindi-Tshopo Region | River (basin) | native | 106290 |
| Little Scarcies | River (basin) | native | 13331 |
| Lower Congo | River (basin) | native | 42510 |
| Lualaba | River (basin) | native | 2970 |
| Malebo Pool | Lake | native | 1879 |
| Marine Lower Congo | River (basin) | native | 1879 |
| Middle Congo | River (basin) | native | 1879 |
| Middle Niger | River (basin) | native | 81285 |
| Moa | River (basin) | native | 13331 |
| Mono | River (basin) | native | 13331 |
| Neotropical | Zoogeographic realm | introduced | 1739 |
| Niger | River (basin) | native | 13331 |
| Niger Delta | River (basin) | native | 81285 |
| Nile | River (basin) | native | 31439 |
| Ogun | River (basin) | native | 81285 |
| Oshun | River (basin) | native | 81285 |
| Ouémé | River (basin) | native | 81285 |
| Pampana | River (basin) | native | 13331 |
| Rokel | River (basin) | native | 81285 |
| Saint John | River (basin) | native | 13331 |
| Saint Paul | River (basin) | native | 13331 |
| Sanaga | River (basin) | native | 81652 |
| Sangha | River (basin) | native | 46233 |
| Sassandra | River (basin) | native | 81285 |
| Senegal | River (basin) | native | 81285 |
| Sewa | River (basin) | native | 81285 |
| Tumba | Lake | native | 41580 |
| Ubangui | River (basin) | native | 45441 |
| Uélé | River (basin) | native | 41590 |
| Upper Lualaba | River (basin) | native | 45616 |
| Victoria | Lake | introduced | 4967 |
| Wagenia Falls | River (basin) | native | 106245 |