| Ekosistem | Type | Status | Acuan |
|---|---|---|---|
| Abaya | Lake | native | 43912 |
| Agnébi | River (basin) | native | 57127 |
| Albert | Lake | native | 43912 |
| Aruwimi | River (basin) | native | 43912 |
| Bandama | River (basin) | native | 57127 |
| Bangweulu | River (basin) | native | 43912 |
| Bani | River (basin) | native | 57127 |
| Benue | River (basin) | native | 43912 |
| Bia | River (basin) | native | 30488 |
| Blue Nile | River (basin) | native | 28714 |
| Boubo | River (basin) | native | 57127 |
| Buzi | River (basin) | native | 43912 |
| Casamance | River (basin) | native | 57127 |
| Chad | River (basin) | native | 57127 |
| Chari-Logone | River (basin) | native | 57127 |
| Chilwa | Lake | native | 43912 |
| Comoé | River (basin) | native | 57127 |
| Congo | River (basin) | native | 43912 |
| Corubal | River (basin) | native | 57127 |
| Cross | River (basin) | native | 57127 |
| Ébrié | Lagoon | native | 43912 |
| Ethiopian | Zoogeographic realm | endemic | 7351 |
| Etosha | Lake | native | 120641 |
| Fitri | Lake | native | 57127 |
| Gambia | River (basin) | native | 57127 |
| Géba | River (basin) | native | 57127 |
| Incomati | River (basin) | native | 43912 |
| Inner Niger Delta | River (basin) | native | 57127 |
| Itimbiri | River (basin) | native | 43912 |
| Kainji | Lake | native | 57127 |
| Kariba | Lake | native | 43912 |
| Kasai | River (basin) | native | 43912 |
| Komadugu Yobe | River (basin) | native | 57127 |
| Kotto | River (basin) | native | 43912 |
| Kunene | River (basin) | native | 43912 |
| Kwa-Ibo | River (basin) | native | 57127 |
| Kwando | River (basin) | native | 33857 |
| Léfini-Likouala | River (basin) | native | 88782 |
| Limpopo | River (basin) | native | 43912 |
| Lindi-Tshopo | River (basin) | native | 43912 |
| Little Scarcies | River (basin) | native | 57127 |
| Lomami | River (basin) | native | 106245 |
| Lower Congo | River (basin) | native | 43912 |
| Lower Niger | River (basin) | native | 57127 |
| Lower Nile | River (basin) | native | 43912 |
| Lower Zambezi | River (basin) | native | 95585 |
| Lualaba | River (basin) | native | 43912 |
| Lukenie | River (basin) | native | 43912 |
| Malagarazi | River (basin) | native | 43912 |
| Malawi | Lake | error | 43912 |
| Maputo | River (basin) | native | 43912 |
| Marine Lower Congo | River (basin) | native | 43912 |
| Middle Congo | River (basin) | native | 43912 |
| Middle Niger | River (basin) | native | 57127 |
| Middle Nile | River (basin) | native | 28714 |
| Middle Zambezi | River (basin) | native | 43912 |
| Mongala | River (basin) | native | 43912 |
| Mono | River (basin) | native | 57127 |
| Mweru | Lake | native | 43912 |
| Niger | River (basin) | native | 57127 |
| Niger Delta | River (basin) | native | 57127 |
| Nile | River (basin) | native | 43912 |
| Northern Ethiopian Rift | Lake | native | 43912 |
| Ogun | River (basin) | native | 57127 |
| Okavango | River (basin) | native | 43912 |
| Oshun | River (basin) | native | 57127 |
| Osse | River (basin) | native | 57127 |
| Ouémé | River (basin) | native | 57127 |
| Pool Malebo | Lake | native | 43912 |
| Pra | River (basin) | native | 57127 |
| Pungwe | River (basin) | native | 43912 |
| Rokel | River (basin) | questionable | 13331 |
| Rufiji | River (basin) | native | 43912 |
| Ruki | River (basin) | native | 43912 |
| Rukwa | Lake | native | 27292 |
| Ruvu | River (basin) | native | 43912 |
| Ruvuma | River (basin) | native | 43912 |
| Sabaki | River (basin) | native | 43912 |
| Sabi | River (basin) | native | 43912 |
| Saloum | River (basin) | native | 57127 |
| Sanaga | River (basin) | native | 81643 |
| Sangha | River (basin) | native | 43912 |
| Sankuru | River (basin) | native | 43912 |
| Sassandra | River (basin) | native | 57127 |
| Senegal | River (basin) | native | 43912 |
| Shabeelle | River (basin) | native | 43912 |
| Shire | River (basin) | native | 43912 |
| Sio | River (basin) | native | 43912 |
| Sokoto | River (basin) | native | 57127 |
| Tana | River (basin) | native | 43912 |
| Tanganyika | Lake | native | 43912 |
| Tano | River (basin) | native | 57127 |
| Turkana | Lake | misidentification | 43912 |
| Ubangui | River (basin) | native | 43912 |
| Uélé | River (basin) | native | 43912 |
| Upper Lualaba | River (basin) | native | 43912 |
| Upper Niger | River (basin) | native | 57127 |
| Upper Zambezi | River (basin) | native | 95585 |
| Victoria | Lake | native | 43912 |
| Victoria Nile | River (basin) | native | 43912 |
| Volta | River (basin) | native | 57127 |
| Wagenia Falls | River (basin) | native | 43912 |
| Wami | River (basin) | native | 43912 |
| White Nile | River (basin) | native | 120561 |
| Wouri | River (basin) | native | 81643 |
| Zambezi | River (basin) | native | 43912 |