| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agnébi | River (basin) | native | 44050 |
| Albert | Lake | native | 44050 |
| Aruwimi | River (basin) | misidentification | 41594 |
| Bandama | River (basin) | native | 57130 |
| Benue | River (basin) | native | 57130 |
| Bia | River (basin) | native | 57130 |
| Blue Nile | River (basin) | native | 28714 |
| Chad | River (basin) | native | 57130 |
| Chari-Logone | River (basin) | native | 44050 |
| Comoé | River (basin) | native | 44050 |
| Congo | River (basin) | misidentification | 44050 |
| Ébrié | Lagoon | native | 57130 |
| Ethiopian | Zoogeographic realm | endemic | 3850 |
| Inner Niger Delta | River (basin) | native | 57130 |
| Itimbiri | River (basin) | misidentification | 41590 |
| Kainji | Lake | native | 44050 |
| Kariba | Lake | misidentification | 44050 |
| Kasai | River (basin) | misidentification | 11970 |
| Komadugu Yobe | River (basin) | native | 57130 |
| Konkouré | River (basin) | native | 57130 |
| Léfini-Likouala | River (basin) | misidentification | 44840 |
| Lower Congo | River (basin) | misidentification | 2264 |
| Lower Niger | River (basin) | native | 57130 |
| Lower Nile | River (basin) | native | 44050 |
| Lualaba | River (basin) | misidentification | 45616 |
| Lukenie | River (basin) | misidentification | 92931 |
| Marine Lower Congo | River (basin) | misidentification | 1879 |
| Middle Congo | River (basin) | misidentification | 41591 |
| Middle Niger | River (basin) | native | 57130 |
| Middle Nile | River (basin) | native | 28714 |
| Niger | River (basin) | native | 57130 |
| Niger Delta | River (basin) | native | 57130 |
| Nile | River (basin) | native | 44050 |
| Pool Malebo | Lake | misidentification | 41585 |
| Pra | River (basin) | native | 44050 |
| Ruki | River (basin) | misidentification | 41580 |
| Sangha | River (basin) | misidentification | 42035 |
| Sankuru | River (basin) | misidentification | 88943 |
| Sassandra | River (basin) | native | 57130 |
| Senegal | River (basin) | native | 57130 |
| Sokoto | River (basin) | native | 57130 |
| Tano | River (basin) | native | 57130 |
| Tumba | Lake | misidentification | 41580 |
| Turkana | Lake | native | 44050 |
| Uélé | River (basin) | misidentification | 41594 |
| Upper Lualaba | River (basin) | misidentification | 45616 |
| Upper Niger | River (basin) | native | 57130 |
| Volta | River (basin) | native | 57130 |
| White Nile | River (basin) | native | 120561 |