| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Bani | River (basin) | native | 57126 |
| Benue | River (basin) | native | 57126 |
| Bia | River (basin) | native | 57126 |
| Blue Nile | River (basin) | native | 28714 |
| Boubo | River (basin) | native | 57126 |
| Chad | River (basin) | native | 57126 |
| Chari-Logone | River (basin) | native | 57126 |
| Chiloango | River (basin) | native | 81642 |
| Comoé | River (basin) | native | 57126 |
| Cross | River (basin) | native | 57126 |
| Ébrié | Lagoon | native | 28587 |
| Ethiopian | Zoogeographic realm | endemic | 3236 |
| Inner Niger Delta | River (basin) | native | 57126 |
| Kainji | Lake | native | 28265 |
| Kienke | River (basin) | native | 81642 |
| Komo | River (basin) | native | 81642 |
| Kouilou-Niari | River (basin) | native | 81642 |
| Loémé | River (basin) | native | 81642 |
| Lower Niger | River (basin) | native | 57126 |
| Mbini | River (basin) | native | 81642 |
| Middle Niger | River (basin) | native | 57126 |
| Middle Nile | River (basin) | native | 28714 |
| Mono | River (basin) | native | 57126 |
| Niger | River (basin) | native | 57126 |
| Niger Delta | River (basin) | native | 57126 |
| Nile | River (basin) | native | 3236 |
| Ntem | River (basin) | native | 81642 |
| Nyanga | River (basin) | native | 81642 |
| Nyong | River (basin) | native | 81642 |
| Ogowe | River (basin) | native | 81642 |
| Ogun | River (basin) | native | 57126 |
| Ouémé | River (basin) | native | 57126 |
| Pra | River (basin) | native | 272 |
| San Pedro | River (basin) | native | 57126 |
| Sanaga | River (basin) | native | 97608 |
| Senegal | River (basin) | native | 57126 |
| Sio | River (basin) | native | 57126 |
| Turkana | Lake | misidentification | 78586 |
| Upper Niger | River (basin) | native | 57126 |
| Volta | River (basin) | native | 57126 |
| White Nile | River (basin) | native | 120561 |
| Wouri | River (basin) | native | 81642 |