| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi River | River (basin) | native | 41594 |
| Bandama | River (basin) | native | 57126 |
| Benue River | River (basin) | native | 13331 |
| Casamance | River (basin) | native | 57126 |
| Chari-Logone System | River (basin) | native | 57126 |
| Comoé | River (basin) | native | 57126 |
| Congo | River (basin) | native | 78218 |
| Corubal | River (basin) | native | 57126 |
| Cross | River (basin) | native | 74661 |
| Ethiopian | Zoogeographic realm | endemic | 6197 |
| Fatala | River (basin) | native | 57126 |
| Gambia | River (basin) | native | 57126 |
| Géba | River (basin) | native | 57126 |
| Great Scarcies | River (basin) | native | 13331 |
| Inner Niger Delta | River (basin) | native | 57126 |
| Itimbiri River | River (basin) | native | 41590 |
| Kainji Lake | Lake | native | 28265 |
| Konkouré | River (basin) | native | 13331 |
| Kwilu River | River (basin) | native | 89725 |
| Lake Rukwa | Lake | native | 27292 |
| Lake Turkana | Lake | native | 52871 |
| Léfini-Likouala Region | River (basin) | native | 88782 |
| Little Scarcies | River (basin) | native | 13331 |
| Lower Congo | River (basin) | native | 42510 |
| Lualaba | River (basin) | native | 45616 |
| Luapula | River (basin) | native | 87720 |
| Malagarazi | River (basin) | native | 36901 |
| Malebo Pool | Lake | native | 41585 |
| Marine Lower Congo | River (basin) | native | 41594 |
| Middle Congo | River (basin) | native | 41590 |
| Middle Niger | River (basin) | native | 57126 |
| Moa | River (basin) | native | 57126 |
| Mweru | Lake | native | 45616 |
| Niger | River (basin) | native | 57126 |
| Niger Delta | River (basin) | native | 57126 |
| Nile | River (basin) | native | 74661 |
| Ogun | River (basin) | native | 57126 |
| Ouémé | River (basin) | native | 13331 |
| Pampana | River (basin) | native | 57126 |
| Ruki River Region | River (basin) | native | 93897 |
| Sankuru | River (basin) | native | 13455 |
| Sassandra | River (basin) | native | 57126 |
| Senegal | River (basin) | native | 57126 |
| Shabeelle | River (basin) | native | 58460 |
| Tanganyika | Lake | native | 36901 |
| Tano | River (basin) | native | 13331 |
| Tumba | Lake | native | 44984 |
| Ubangui | River (basin) | native | 45441 |
| Uélé | River (basin) | native | 41594 |
| Upper Lualaba | River (basin) | native | 45616 |
| Upper Niger | River (basin) | native | 57126 |