| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 41590 |
| Bangweulu | River (basin) | native | 42135 |
| Benue | River (basin) | native | 367 |
| Chad | River (basin) | misidentification | 367 |
| Congo | River (basin) | native | 2970 |
| Cross | River (basin) | native | 271 |
| Cuanza | River (basin) | native | 1878 |
| Ethiopian | Zoogeographic realm | endemic | 3203 |
| Fatala | River (basin) | misidentification | 3009 |
| Géba | River (basin) | native | 1880 |
| Itimbiri | River (basin) | native | 41590 |
| Kasai | River (basin) | native | 41590 |
| Kienke | River (basin) | native | 41590 |
| Konkouré | River (basin) | misidentification | 3009 |
| Kouilou-Niari | River (basin) | questionable | 87308 |
| Lindi-Tshopo | River (basin) | native | 42183 |
| Lofa | River (basin) | native | 3046 |
| Lower Congo | River (basin) | native | 42510 |
| Lualaba | River (basin) | native | 45616 |
| Mai-Ndombe | Lake | native | 1878 |
| Mbini | River (basin) | questionable | 87308 |
| Middle Congo | River (basin) | native | 4910 |
| Moa | River (basin) | native | 3046 |
| Mweru | Lake | native | 27609 |
| Ntem | River (basin) | native | 27896 |
| Nyanga | River (basin) | native | 52344 |
| Nyong | River (basin) | native | 51193 |
| Ogowe | River (basin) | native | 1878 |
| Ogun | River (basin) | native | 1880 |
| Okavango | River (basin) | native | 11970 |
| Pampana | River (basin) | native | 3046 |
| Pool Malebo | Lake | native | 41585 |
| Ruki | River (basin) | native | 41580 |
| Saint John | River (basin) | native | 3046 |
| Saint Paul | River (basin) | native | 3046 |
| Sanaga | River (basin) | misidentification | 47417 |
| Sangha | River (basin) | native | 46233 |
| Sewa | River (basin) | native | 3046 |
| Tumba | Lake | native | 41580 |
| Ubangui | River (basin) | native | 45441 |
| Uélé | River (basin) | native | 1879 |
| Upper Lualaba | River (basin) | native | 2970 |
| Upper Niger | River (basin) | misidentification | 2756 |
| Upper Zambezi | River (basin) | native | 11970 |
| Wagenia Falls | River (basin) | native | 106245 |
| Zambezi | River (basin) | native | 11970 |