| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Albert | Lake | native | 52193 |
| Aruwimi | River (basin) | native | 106290 |
| Bandama | River (basin) | native | 272 |
| Bangweulu | River (basin) | native | 42135 |
| Benue | River (basin) | native | 28663 |
| Bia | River (basin) | native | 272 |
| Blue Nile | River (basin) | native | 28714 |
| Buzi | River (basin) | native | 52193 |
| Cavally | River (basin) | native | 13331 |
| Chad | River (basin) | native | 28663 |
| Comoé | River (basin) | native | 272 |
| Congo | River (basin) | native | 52193 |
| Corubal | River (basin) | native | 13331 |
| Cross | River (basin) | native | 13331 |
| Ébrié | Lagoon | native | 272 |
| Ethiopian | Zoogeographic realm | endemic | 2915 |
| Fatala | River (basin) | native | 28587 |
| Gambia | River (basin) | native | 28663 |
| Géba | River (basin) | native | 13331 |
| Itimbiri | River (basin) | native | 106290 |
| Kariba | Lake | native | 39194 |
| Kasai | River (basin) | native | 11970 |
| Kogon | River (basin) | native | 13331 |
| Konkouré | River (basin) | native | 13331 |
| Kwango | River (basin) | native | 11970 |
| Kwilu | River (basin) | native | 11970 |
| Lindi-Tshopo | River (basin) | native | 106290 |
| Lofa | River (basin) | native | 13331 |
| Lower Congo | River (basin) | native | 42510 |
| Lualaba | River (basin) | native | 45616 |
| Mai-Ndombe | Lake | native | 1878 |
| Malawi | Lake | native | 55909 |
| Marine Lower Congo | River (basin) | native | 1878 |
| Middle Congo | River (basin) | native | 4910 |
| Middle Nile | River (basin) | native | 28714 |
| Middle Zambezi | River (basin) | native | 113554 |
| Moa | River (basin) | native | 13331 |
| Mono | River (basin) | native | 13331 |
| Mweru | Lake | native | 27609 |
| Niger | River (basin) | native | 28663 |
| Nile | River (basin) | native | 52193 |
| Ogun | River (basin) | native | 13331 |
| Ouémé | River (basin) | native | 13331 |
| Pool Malebo | Lake | native | 41585 |
| Pra | River (basin) | native | 272 |
| Pungwe | River (basin) | native | 52193 |
| Rokel | River (basin) | native | 13331 |
| Ruki | River (basin) | native | 93897 |
| Saint John | River (basin) | native | 2915 |
| Saint Paul | River (basin) | native | 2915 |
| Sanaga | River (basin) | native | 51193 |
| Sangha | River (basin) | native | 46233 |
| Sankuru | River (basin) | native | 13455 |
| Sassandra | River (basin) | native | 272 |
| Senegal | River (basin) | native | 28663 |
| Sewa | River (basin) | native | 13331 |
| Shire | River (basin) | native | 37112 |
| Tanganyika | Lake | native | 52193 |
| Tumba | Lake | native | 41580 |
| Ubangui | River (basin) | native | 45441 |
| Uélé | River (basin) | native | 41590 |
| Upper Lualaba | River (basin) | native | 2970 |
| Volta | River (basin) | native | 28663 |
| Wagenia Falls | River (basin) | native | 106245 |
| White Nile | River (basin) | native | 120561 |
| Zambezi | River (basin) | native | 52193 |