| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agnébi | River (basin) | native | 13331 |
| Bandama | River (basin) | native | 13331 |
| Banio | River (basin) | native | 81647 |
| Bengo | River (basin) | native | 120641 |
| Bia | River (basin) | native | 13331 |
| Bioko | River (basin) | native | 81647 |
| Boubo | River (basin) | native | 57259 |
| Cacheu | River (basin) | native | 57259 |
| Casamance | River (basin) | native | 33587 |
| Cavally | River (basin) | native | 13331 |
| Cess | River (basin) | native | 13331 |
| Chiloango | River (basin) | native | 41597 |
| Comoé | River (basin) | native | 13331 |
| Congo | River (basin) | native | 47311 |
| Corubal | River (basin) | native | 13331 |
| Cross | River (basin) | native | 13331 |
| Cuanza | River (basin) | native | 120641 |
| Densu | River (basin) | native | 57259 |
| Dibamba | River (basin) | native | 81647 |
| Ébrié | Lagoon | native | 28587 |
| Ethiopian | Zoogeographic realm | endemic | 3788 |
| Farmington | River (basin) | native | 13331 |
| Fatala | River (basin) | native | 57259 |
| Gambia | River (basin) | native | 13331 |
| Géba | River (basin) | native | 13331 |
| Great Scarcies | River (basin) | native | 13331 |
| Kienke | River (basin) | native | 81647 |
| Kogon | River (basin) | native | 13331 |
| Komo | River (basin) | native | 81647 |
| Konkouré | River (basin) | native | 13331 |
| Kouilou-Niari | River (basin) | native | 40404 |
| Little Scarcies | River (basin) | native | 13331 |
| Loémé | River (basin) | native | 81647 |
| Lofa | River (basin) | native | 13331 |
| Lokoundje | River (basin) | native | 47441 |
| Marine Lower Congo | River (basin) | native | 1879 |
| Mbini | River (basin) | native | 81647 |
| Moa | River (basin) | native | 13331 |
| Mono | River (basin) | native | 13331 |
| Muni | River (basin) | native | 81647 |
| Ndogo | River (basin) | native | 81647 |
| Niger | River (basin) | native | 13331 |
| Nkomi | River (basin) | native | 81647 |
| Ntem | River (basin) | native | 81647 |
| Nyanga | River (basin) | native | 81647 |
| Ogowe | River (basin) | native | 80286 |
| Ogun | River (basin) | native | 13331 |
| Oshun | River (basin) | native | 57259 |
| Osse | River (basin) | native | 57259 |
| Ouémé | River (basin) | native | 13331 |
| Pra | River (basin) | native | 13331 |
| Rio del Rey | River (basin) | native | 81647 |
| Rokel | River (basin) | native | 13331 |
| Saint John | River (basin) | native | 13331 |
| Saint Paul | River (basin) | native | 13331 |
| Saloum | River (basin) | native | 28587 |
| San Pedro | River (basin) | native | 57259 |
| Sanaga | River (basin) | native | 51193 |
| Sassandra | River (basin) | native | 13331 |
| Senegal | River (basin) | native | 57259 |
| Sewa | River (basin) | native | 13331 |
| Sio | River (basin) | native | 57259 |
| Tano | River (basin) | native | 13331 |
| Volta | River (basin) | native | 13331 |
| Wouri | River (basin) | native | 81647 |