| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Albert | Lake | native | 4903 |
| Aruwimi River | River (basin) | native | 106290 |
| Benue River | River (basin) | native | 81279 |
| Chobe | River (basin) | native | 37065 |
| Congo | River (basin) | native | 93897 |
| Cross | River (basin) | native | 81279 |
| Ethiopian | Zoogeographic realm | endemic | 2880 |
| Itimbiri River | River (basin) | native | 106290 |
| Kariba | Lake | native | 39194 |
| Kasai River | River (basin) | native | 11970 |
| Kunene | River (basin) | native | 33857 |
| Kwando River | River (basin) | native | 37065 |
| Kwango River | River (basin) | native | 11970 |
| Kwilu River | River (basin) | native | 89725 |
| Lake Rukwa | Lake | native | 95585 |
| Lake Turkana | Lake | native | 28663 |
| Liambezi | Lake | native | 37065 |
| Limpopo | River (basin) | native | 13332 |
| Lindi-Tshopo Region | River (basin) | native | 106290 |
| Lower Congo | River (basin) | native | 42510 |
| Lower Zambezi | River (basin) | native | 95585 |
| Lualaba | River (basin) | native | 45434 |
| Luapula | River (basin) | native | 95585 |
| Mai-Ndombe | Lake | native | 88943 |
| Malagarazi | River (basin) | native | 98755 |
| Malebo Pool | Lake | native | 41585 |
| Middle Congo | River (basin) | native | 4910 |
| Middle Zambezi | River (basin) | native | 95585 |
| Mono | River (basin) | native | 81279 |
| Mweru | Lake | native | 45616 |
| Niger | River (basin) | native | 81279 |
| Nile | River (basin) | native | 28663 |
| Okavango | River (basin) | native | 7248 |
| Ouémé | River (basin) | native | 81279 |
| Pra | River (basin) | native | 272 |
| Ruki River Region | River (basin) | native | 93897 |
| Sanaga | River (basin) | native | 80290 |
| Sangha | River (basin) | native | 44840 |
| Sankuru | River (basin) | native | 88943 |
| Senegal | River (basin) | native | 81279 |
| Shire | River (basin) | native | 37112 |
| Tanganyika | Lake | native | 36901 |
| Tumba | Lake | native | 41580 |
| Ubangui | River (basin) | native | 45441 |
| Uélé | River (basin) | native | 41594 |
| Upper Lualaba | River (basin) | native | 45434 |
| Upper Zambezi | River (basin) | native | 95585 |
| Victoria-Nile | River (basin) | native | 4903 |
| Wagenia Falls | River (basin) | native | 106245 |
| White Nile | River (basin) | native | 4903 |
| Zambezi | River (basin) | native | 13332 |