| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Abaya | Lake | native | 248 |
| Australian | Zoogeographic realm | introduced | 78572 |
| Awash | River (basin) | native | 248 |
| Bandama | River (basin) | native | 57129 |
| Baraka | River (basin) | native | 248 |
| Baringo | Lake | native | 248 |
| Bengo | River (basin) | native | 248 |
| Benue River | River (basin) | native | 57129 |
| Bushmans | River (basin) | introduced | 6465 |
| Buzi | River (basin) | native | 13332 |
| Cape | River (basin) | introduced | 6465 |
| Chari-Logone System | River (basin) | native | 57129 |
| Chiloango | River (basin) | questionable | 92874 |
| Chobe | River (basin) | native | 37065 |
| Comoé | River (basin) | native | 57129 |
| Congo | River (basin) | native | 248 |
| Corubal | River (basin) | native | 57129 |
| Cross | River (basin) | questionable | 85170 |
| Cuanza | River (basin) | native | 248 |
| Cyrenaica coast | River (basin) | native | 248 |
| Da River | River (basin) | introduced | 89724 |
| Dillia | River (basin) | native | 57129 |
| Don | River (basin) | questionable | 58293 |
| Ébrié Lagoon | Lagoon | native | 57129 |
| Edward | Lake | native | 248 |
| Ethiopian | Zoogeographic realm | native | 248 |
| Fitri | Lake | native | 57129 |
| Great Fish | River (basin) | introduced | 92875 |
| Great Kei | River (basin) | introduced | 6465 |
| Incomati | River (basin) | native | 92875 |
| Inner Niger Delta | River (basin) | native | 57129 |
| Kainji Lake | Lake | native | 28265 |
| Kariba | Lake | native | 39194 |
| Kasai River | River (basin) | native | 248 |
| Keiskama | River (basin) | introduced | 92875 |
| Kivu | Lake | native | 248 |
| Komadugu Yobe | River (basin) | native | 57129 |
| Konkouré | River (basin) | native | 57129 |
| Kouilou-Niari | River (basin) | introduced | 81644 |
| Kunene | River (basin) | native | 33857 |
| Kwa-Ibo | River (basin) | native | 57129 |
| Kwando River | River (basin) | native | 37065 |
| Kwango River | River (basin) | native | 248 |
| Laguna de Bay | Lake | introduced | 13446 |
| Lake Malawi | Lake | native | 55909 |
| Lake Rukwa | Lake | native | 27292 |
| Lake Turkana | Lake | native | 52871 |
| Liambezi | Lake | native | 37065 |
| Limpopo | River (basin) | native | 13332 |
| Lindi-Tshopo Region | River (basin) | native | 248 |
| Linyanti Swamp | Lake | native | 37065 |
| Lower Congo | River (basin) | native | 101841 |
| Lower Niger | River (basin) | native | 57129 |
| Lower Zambezi | River (basin) | native | 95585 |
| Lualaba | River (basin) | native | 248 |
| Luapula | River (basin) | native | 248 |
| Malagarazi | River (basin) | native | 248 |
| Malebo Pool | Lake | native | 101841 |
| Marine Lower Congo | River (basin) | native | 248 |
| Mekong | River (basin) | introduced | 12693 |
| Melrhir | River (basin) | native | 248 |
| Middle Congo | River (basin) | native | 248 |
| Middle Niger | River (basin) | native | 57129 |
| Middle Zambezi | River (basin) | native | 95585 |
| Mono | River (basin) | native | 57129 |
| Mweru | Lake | native | 248 |
| Neotropical | Zoogeographic realm | introduced | 56821 |
| Niger | River (basin) | native | 57129 |
| Niger Delta | River (basin) | native | 57129 |
| Nile | River (basin) | native | 248 |
| Ogowe | River (basin) | introduced | 81644 |
| Ogun | River (basin) | native | 57129 |
| Okavango | River (basin) | native | 27501 |
| Orange | River (basin) | native | 33857 |
| Oriental | Zoogeographic realm | introduced | 43640 |
| Oshun | River (basin) | native | 57129 |
| Osse | River (basin) | native | 248 |
| Ouémé | River (basin) | native | 57129 |
| Palearctic | Zoogeographic realm | native | 248 |
| Pangani | River (basin) | native | 248 |
| Pongolo | River (basin) | native | 92875 |
| Pungwe | River (basin) | native | 92875 |
| Rufiji | River (basin) | native | 248 |
| Rusizi | River (basin) | native | 248 |
| Ruvu | River (basin) | native | 248 |
| Ruvuma River | River (basin) | native | 13332 |
| Sabaki | River (basin) | native | 30558 |
| Sabi | River (basin) | native | 248 |
| Sahara | River (basin) | native | 57129 |
| Saint Lucia | River (basin) | native | 92875 |
| Sanaga | River (basin) | native | 81644 |
| Sankuru | River (basin) | native | 248 |
| Senegal | River (basin) | native | 57129 |
| Shabeelle | River (basin) | native | 248 |
| Shire | River (basin) | native | 37112 |
| Sio | River (basin) | native | 248 |
| Sokoto | River (basin) | native | 57129 |
| Sundays | River (basin) | introduced | 92875 |
| Tana River | River (basin) | native | 13332 |
| Tanganyika | Lake | native | 248 |
| Tugela | River (basin) | native | 92875 |
| Ubangui | River (basin) | native | 248 |
| Uélé | River (basin) | native | 248 |
| Umbuluzi | River (basin) | native | 92875 |
| Umfolosi | River (basin) | native | 92875 |
| Umgeni | River (basin) | native | 248 |
| Umkomaas | River (basin) | native | 248 |
| Umtamvuna | River (basin) | native | 92874 |
| Umzimkulu | River (basin) | native | 92875 |
| Upper Lualaba | River (basin) | native | 248 |
| Upper Niger | River (basin) | native | 57129 |
| Upper Zambezi | River (basin) | native | 95585 |
| Uruguay | River (basin) | introduced | 79585 |
| Victoria | Lake | native | 34290 |
| Victoria-Nile | River (basin) | native | 4903 |
| Voi | River (basin) | native | 248 |
| Wagenia Falls | River (basin) | native | 248 |
| Wami | River (basin) | native | 13332 |
| White Nile | River (basin) | native | 4903 |
| Zambezi | River (basin) | native | 13332 |
| Zanzibar | River (basin) | native | 248 |