| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agnébi | River (basin) | native | 272 |
| Albert | Lake | native | 43912 |
| Aruwimi | River (basin) | misidentification | 43912 |
| Bandama | River (basin) | native | 272 |
| Bani | River (basin) | native | 57127 |
| Benue | River (basin) | native | 57127 |
| Blue Nile | River (basin) | native | 43912 |
| Chad | River (basin) | native | 57127 |
| Chari-Logone | River (basin) | native | 57127 |
| Comoé | River (basin) | native | 272 |
| Congo | River (basin) | misidentification | 43912 |
| Corubal | River (basin) | native | 57127 |
| Cross | River (basin) | native | 57127 |
| Ébrié | Lagoon | native | 28587 |
| Ethiopian | Zoogeographic realm | endemic | 3570 |
| Gambia | River (basin) | error | 43912 |
| Géba | River (basin) | native | 57127 |
| Great Scarcies | River (basin) | native | 57127 |
| Inner Niger Delta | River (basin) | native | 57127 |
| Kainji | Lake | native | 57127 |
| Kwa-Ibo | River (basin) | native | 57127 |
| Kwando | River (basin) | misidentification | 43912 |
| Little Scarcies | River (basin) | native | 57127 |
| Lofa | River (basin) | native | 57127 |
| Lower Niger | River (basin) | native | 57127 |
| Lower Nile | River (basin) | native | 43912 |
| Mano | River (basin) | native | 81643 |
| Middle Congo | River (basin) | misidentification | 43912 |
| Middle Niger | River (basin) | native | 57127 |
| Middle Nile | River (basin) | native | 28714 |
| Moa | River (basin) | native | 57127 |
| Mono | River (basin) | native | 57127 |
| Niger | River (basin) | native | 57127 |
| Niger Delta | River (basin) | native | 57127 |
| Nile | River (basin) | native | 28714 |
| Nile Delta | River (basin) | native | 43912 |
| Ogowe | River (basin) | misidentification | 43912 |
| Ogun | River (basin) | native | 57127 |
| Oshun | River (basin) | native | 57127 |
| Ouémé | River (basin) | native | 57127 |
| Pampana | River (basin) | native | 57127 |
| Pool Malebo | Lake | misidentification | 96563 |
| Rukwa | Lake | questionable | 4967 |
| Saint Paul | River (basin) | native | 57127 |
| Sanaga | River (basin) | native | 81643 |
| Sassandra | River (basin) | native | 272 |
| Semliki | River (basin) | native | 43912 |
| Senegal | River (basin) | native | 57127 |
| Sokoto | River (basin) | native | 57127 |
| Tana | River (basin) | misidentification | 32384 |
| Tano | River (basin) | native | 272 |
| Ubangui | River (basin) | misidentification | 43912 |
| Uélé | River (basin) | misidentification | 43912 |
| Upper Niger | River (basin) | native | 57127 |
| Victoria | Lake | questionable | 4967 |
| Volta | River (basin) | native | 57127 |
| White Nile | River (basin) | native | 120561 |
| Wouri | River (basin) | native | 81643 |
| Zambezi | River (basin) | misidentification | 3570 |