| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Awash | River (basin) | native | 58460 |
| Bangweulu | River (basin) | native | 41590 |
| Baringo | Lake | native | 52331 |
| Chobe | River (basin) | native | 37065 |
| Congo | River (basin) | native | 45434 |
| Cuanza | River (basin) | native | 7248 |
| Ethiopian | Zoogeographic realm | endemic | 2801 |
| Etosha | Lake | native | 120641 |
| Kasai | River (basin) | native | 42554 |
| Kunene | River (basin) | native | 52863 |
| Kwando | River (basin) | native | 37065 |
| Liambezi | Lake | native | 37065 |
| Limpopo | River (basin) | native | 13332 |
| Linyanti Swamp | Lake | native | 37065 |
| Lomami | River (basin) | native | 12818 |
| Lower Zambezi | River (basin) | native | 95585 |
| Malagarazi | River (basin) | native | 54847 |
| Malawi | Lake | native | 55909 |
| Middle Zambezi | River (basin) | native | 95585 |
| Mweru | Lake | native | 41590 |
| Okavango | River (basin) | native | 27501 |
| Orange | River (basin) | native | 33857 |
| Pangani | River (basin) | native | 52331 |
| Rufiji | River (basin) | native | 93960 |
| Rukwa | Lake | native | 27292 |
| Sabaki | River (basin) | native | 52331 |
| Sankuru | River (basin) | native | 12818 |
| Shire | River (basin) | native | 37112 |
| Tana | River (basin) | native | 52331 |
| Tana | Lake | native | 128753 |
| Turkana | Lake | native | 31508 |
| Upper Lualaba | River (basin) | native | 45434 |
| Upper Zambezi | River (basin) | native | 95585 |
| Victoria | Lake | native | 4903 |
| Victoria Nile | River (basin) | native | 4903 |
| Voi | River (basin) | native | 30558 |
| Wami | River (basin) | native | 93960 |
| Zambezi | River (basin) | native | 13332 |