| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | questionable | 41594 |
| Bangweulu | River (basin) | native | 45616 |
| Coastal Southwest Angola | River (basin) | native | 11970 |
| Congo | River (basin) | native | 26192 |
| Coroca | River (basin) | native | 11970 |
| Cuanza | River (basin) | native | 11970 |
| Ethiopian | Zoogeographic realm | endemic | 2801 |
| Kariba | Lake | native | 39194 |
| Kunene | River (basin) | native | 89016 |
| Limpopo | River (basin) | native | 13337 |
| Lualaba | River (basin) | native | 26192 |
| Malagarazi | River (basin) | native | 26192 |
| Malawi | Lake | native | 4967 |
| Maputo | River (basin) | native | 94784 |
| Mweru | Lake | native | 26192 |
| Okavango | River (basin) | native | 27501 |
| Rukwa | Lake | native | 27292 |
| Rusizi | River (basin) | native | 26192 |
| Sabaki | River (basin) | native | 30558 |
| Shire | River (basin) | native | 37112 |
| Tana | River (basin) | native | 13332 |
| Tanganyika | Lake | native | 26192 |
| Turkana | Lake | native | 52331 |
| Upper Lualaba | River (basin) | native | 26192 |
| Wagenia Falls | River (basin) | native | 106245 |
| Zambezi | River (basin) | native | 13337 |