| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Bangweulu | River (basin) | native | 95585 |
| Chad | River (basin) | native | 47311 |
| Chobe | River (basin) | native | 47311 |
| Congo | River (basin) | native | 47311 |
| Ethiopian | Zoogeographic realm | endemic | 3788 |
| Itimbiri | River (basin) | native | 47311 |
| Kasai | River (basin) | native | 47311 |
| Kotto | River (basin) | native | 47311 |
| Kwando | River (basin) | native | 47311 |
| Kwilu | River (basin) | native | 11970 |
| Liambezi | Lake | native | 37065 |
| Linyanti Swamp | Lake | native | 37065 |
| Lomami | River (basin) | native | 47311 |
| Lower Zambezi | River (basin) | native | 95585 |
| Lualaba | River (basin) | native | 47311 |
| Middle Zambezi | River (basin) | native | 95585 |
| Mweru | Lake | native | 95585 |
| Nile | River (basin) | native | 47311 |
| Okavango | River (basin) | native | 27501 |
| Sankuru | River (basin) | native | 47311 |
| Shire | River (basin) | native | 47311 |
| Ubangui | River (basin) | native | 47311 |
| Uélé | River (basin) | native | 47311 |
| Upper Lualaba | River (basin) | native | 47311 |
| Upper Zambezi | River (basin) | native | 95585 |
| Wagenia Falls | River (basin) | native | 106245 |
| Zambezi | River (basin) | native | 47311 |