| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agnébi | River (basin) | native | 13331 |
| Ankobra | River (basin) | native | 57413 |
| Bandama | River (basin) | native | 57413 |
| Benue | River (basin) | native | 57413 |
| Bia | River (basin) | native | 57413 |
| Cavally | River (basin) | native | 57413 |
| Cess | River (basin) | native | 57413 |
| Chad | River (basin) | native | 57413 |
| Chari-Logone | River (basin) | native | 57413 |
| Comoé | River (basin) | native | 57413 |
| Congo | River (basin) | native | 81660 |
| Corubal | River (basin) | native | 13331 |
| Cross | River (basin) | native | 57413 |
| Densu | River (basin) | native | 57413 |
| Ébrié | Lagoon | native | 57413 |
| Ethiopian | Zoogeographic realm | endemic | 6802 |
| Gambia | River (basin) | questionable | 28587 |
| Great Scarcies | River (basin) | native | 57413 |
| Inner Niger Delta | River (basin) | native | 57413 |
| Itimbiri | River (basin) | native | 106290 |
| Kogon | River (basin) | native | 13331 |
| Konkouré | River (basin) | native | 57413 |
| Little Scarcies | River (basin) | native | 57413 |
| Lomami | River (basin) | native | 46861 |
| Lower Congo | River (basin) | native | 41585 |
| Lower Niger | River (basin) | native | 57413 |
| Lualaba | River (basin) | native | 93587 |
| Middle Congo | River (basin) | native | 4910 |
| Moa | River (basin) | native | 57413 |
| Niger | River (basin) | native | 57413 |
| Niger Delta | River (basin) | native | 57413 |
| Nile | River (basin) | native | 28714 |
| Ntem | River (basin) | native | 81660 |
| Nyong | River (basin) | native | 81660 |
| Oshun | River (basin) | native | 57413 |
| Ouémé | River (basin) | questionable | 13331 |
| Pampana | River (basin) | native | 57413 |
| Pool Malebo | Lake | native | 41585 |
| Rokel | River (basin) | native | 57413 |
| Ruki | River (basin) | native | 41580 |
| Saint John | River (basin) | native | 57413 |
| Sanaga | River (basin) | native | 81660 |
| Sangha | River (basin) | native | 46233 |
| Sassandra | River (basin) | native | 57413 |
| Senegal | River (basin) | native | 57413 |
| Sewa | River (basin) | native | 57413 |
| Tano | River (basin) | native | 13331 |
| Tumba | Lake | native | 41580 |
| Ubangui | River (basin) | native | 45441 |
| Upper Lualaba | River (basin) | native | 41590 |
| Upper Niger | River (basin) | native | 57413 |
| Volta | River (basin) | native | 57413 |
| Wagenia Falls | River (basin) | native | 106245 |
| White Nile | River (basin) | native | 120561 |