| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi River | River (basin) | native | 106290 |
| Bandama | River (basin) | native | 13331 |
| Benue River | River (basin) | native | 53405 |
| Bia | River (basin) | native | 13331 |
| Cavally | River (basin) | native | 13331 |
| Cess | River (basin) | native | 13331 |
| Comoé | River (basin) | native | 13331 |
| Congo | River (basin) | native | 55074 |
| Corubal | River (basin) | native | 13331 |
| Cross | River (basin) | native | 85170 |
| Erhjen River | River (basin) | introduced | 36073 |
| Ethiopian | Zoogeographic realm | endemic | 88 |
| Itimbiri River | River (basin) | native | 106290 |
| Kainji Lake | Lake | native | 28265 |
| Kaoping River | River (basin) | introduced | 36073 |
| Konkouré | River (basin) | native | 13331 |
| Laguna de Bay | Lake | introduced | |
| Lake Turkana | Lake | introduced | 52871 |
| Lindi-Tshopo Region | River (basin) | native | 106290 |
| Little Scarcies | River (basin) | native | 13331 |
| Lofa | River (basin) | native | 13331 |
| Middle Congo | River (basin) | native | 55074 |
| Moa | River (basin) | native | 13331 |
| Mongala | River (basin) | native | 55074 |
| Mono | River (basin) | native | 13331 |
| Nearctic | Zoogeographic realm | introduced | 3814 |
| Neotropical | Zoogeographic realm | introduced | 1739 |
| Niger | River (basin) | native | 53405 |
| Nile | River (basin) | native | 5163 |
| Ogun | River (basin) | native | 31256 |
| Oriental | Zoogeographic realm | introduced | 5193 |
| Ouémé | River (basin) | native | 28663 |
| Palearctic | Zoogeographic realm | introduced | 5163 |
| Red Sea | Sea/Bay/Gulf | native | 84159 |
| Rokel | River (basin) | introduced | 1739 |
| Saint John | River (basin) | native | 13331 |
| Saint Paul | River (basin) | native | 13331 |
| Sanaga | River (basin) | native | 51193 |
| Sassandra | River (basin) | native | 13331 |
| Senegal | River (basin) | native | 53405 |
| Tana River | River (basin) | introduced | 52331 |
| Tano | River (basin) | native | 272 |
| Tigris | River (basin) | introduced | 39702 |
| Tsengwen River | River (basin) | introduced | 36073 |
| Ubangui | River (basin) | native | 55074 |
| Uélé | River (basin) | native | 55074 |
| Victoria | Lake | introduced | 4967 |
| Wagenia Falls | River (basin) | native | 106245 |