| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Acheloos | River (basin) | introduced | 59043 |
| Albert | Lake | native | 52307 |
| Aruwimi | River (basin) | introduced | 2 |
| Awash | River (basin) | native | 52307 |
| Baringo | Lake | native | 52307 |
| Benue | River (basin) | native | 13331 |
| Bia | River (basin) | native | 272 |
| Blue Nile | River (basin) | native | 28714 |
| Cess | River (basin) | native | 272 |
| Chad | River (basin) | native | 53405 |
| Chiku River | River (basin) | introduced | 36073 |
| Comoé | River (basin) | native | 272 |
| Congo | River (basin) | introduced | 1739 |
| Cross | River (basin) | native | 53784 |
| Da River | River (basin) | introduced | 89724 |
| Ébrié | Lagoon | native | 28587 |
| Edward | Lake | native | 52307 |
| Ethiopian | Zoogeographic realm | endemic | 5166 |
| Gambia | River (basin) | native | 53405 |
| Itimbiri | River (basin) | introduced | 106290 |
| Kainji | Lake | native | 28265 |
| Kaoping River | River (basin) | introduced | 36073 |
| Kariba | Lake | introduced | 27602 |
| Kivu | Lake | native | 107916 |
| Laguna de Bay | Lake | introduced | 6096 |
| Lake Lanao | Lake | introduced | 10888 |
| Lake Mainit | Lake | introduced | 4867 |
| Lindi-Tshopo | River (basin) | introduced | 106290 |
| Lower Congo | River (basin) | introduced | 2 |
| Lualaba | River (basin) | introduced | 55074 |
| Lukuledi | River (basin) | introduced | 118630 |
| Magdalena | River (basin) | introduced | 78646 |
| Malawi | Lake | introduced | 118630 |
| Mbwemburu | River (basin) | introduced | 118630 |
| Mekong | River (basin) | introduced | 12693 |
| Middle Congo | River (basin) | introduced | 55074 |
| Middle Nile | River (basin) | native | 28714 |
| Nakdong | River (basin) | introduced | 58345 |
| Naujan Lake | Lake | introduced | 13446 |
| Nearctic | Zoogeographic realm | introduced | 166 |
| Neotropical | Zoogeographic realm | introduced | 5166 |
| Niger | River (basin) | native | 53405 |
| Nile | River (basin) | native | 28714 |
| Oriental | Zoogeographic realm | introduced | 13686 |
| Palearctic | Zoogeographic realm | introduced | 5166 |
| Pangani | River (basin) | introduced | 118630 |
| Pra | River (basin) | native | 13331 |
| Rufiji | River (basin) | introduced | 118630 |
| Rukwa | Lake | introduced | 118630 |
| Rusizi | River (basin) | native | 52307 |
| Ruvu | River (basin) | introduced | 118630 |
| Senegal | River (basin) | native | 53405 |
| Southern East Rift Valley | Lake | introduced | 118630 |
| Taal Lake | Lake | introduced | 12165 |
| Tana | Lake | native | 96382 |
| Tanganyika | Lake | native | 107916 |
| Tigris | River (basin) | introduced | 39702 |
| Toba | Lake | introduced | 57970 |
| Turkana | Lake | native | 27629 |
| Uélé | River (basin) | introduced | 2 |
| Upper Lualaba | River (basin) | introduced | 55074 |
| Uruguay | River (basin) | introduced | 79585 |
| Victoria | Lake | introduced | 1739 |
| Voi | River (basin) | introduced | 118630 |
| Volta | River (basin) | native | 53405 |
| Wagenia Falls | River (basin) | introduced | 106245 |
| Wami | River (basin) | introduced | 118630 |
| White Nile | River (basin) | native | 120561 |
| Yili River | River (basin) | introduced | 41093 |
| Zanzibar | River (basin) | introduced | 118630 |