| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi River | River (basin) | native | 106290 |
| Australian | Zoogeographic realm | introduced | 9420 |
| Benue River | River (basin) | questionable | 51193 |
| Catumbela | River (basin) | native | 11970 |
| Chiloango | River (basin) | introduced | 55074 |
| Chobe | River (basin) | native | 37065 |
| Coastal Southwest Angola | River (basin) | native | 11970 |
| Congo | River (basin) | native | 55074 |
| Cuanza | River (basin) | native | 11970 |
| Ethiopian | Zoogeographic realm | endemic | 21 |
| Kariba | Lake | native | 39194 |
| Kasai River | River (basin) | native | 55074 |
| Kivu | Lake | introduced | 27629 |
| Kunene | River (basin) | native | 3091 |
| Kwando River | River (basin) | native | 37065 |
| Lake Malawi | Lake | native | 34290 |
| Lake Rukwa | Lake | native | 27292 |
| Liambezi | Lake | native | 37065 |
| Limpopo | River (basin) | native | 13332 |
| Lindi-Tshopo Region | River (basin) | native | 106290 |
| Linyanti Swamp | Lake | native | 37065 |
| Lomami River | River (basin) | native | 106245 |
| Lower Congo | River (basin) | introduced | 55074 |
| Lower Zambezi | River (basin) | native | 95585 |
| Lualaba | River (basin) | native | 106245 |
| Luapula | River (basin) | native | 55074 |
| Machado | River (basin) | introduced | 97589 |
| Malagarazi | River (basin) | native | 55074 |
| Middle Congo | River (basin) | native | 106245 |
| Middle Zambezi | River (basin) | native | 95585 |
| Mweru | Lake | native | 55074 |
| Neotropical | Zoogeographic realm | introduced | 21 |
| Ogowe | River (basin) | introduced | 82489 |
| Okavango | River (basin) | native | 74387 |
| Orange | River (basin) | native | 33857 |
| Oriental | Zoogeographic realm | introduced | 1739 |
| Sabaki | River (basin) | introduced | 30558 |
| Sanaga | River (basin) | introduced | 82489 |
| Sankuru | River (basin) | native | 55074 |
| Shire | River (basin) | native | 37112 |
| Tana River | River (basin) | introduced | 52331 |
| Tanganyika | Lake | native | 21 |
| Uélé | River (basin) | native | 55074 |
| Upper Lualaba | River (basin) | native | 55074 |
| Upper Zambezi | River (basin) | native | 95585 |
| Victoria | Lake | introduced | 34290 |
| Wagenia Falls | River (basin) | native | 106245 |
| Zambezi | River (basin) | native | 13332 |