| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | questionable | 106290 |
| Banio | River (basin) | native | 81639 |
| Bengo | River (basin) | native | 120641 |
| Chad | River (basin) | native | 367 |
| Chiloango | River (basin) | native | 81639 |
| Congo | River (basin) | native | 41590 |
| Cuanza | River (basin) | native | 120641 |
| Ethiopian | Zoogeographic realm | endemic | 2801 |
| Itimbiri | River (basin) | native | 106290 |
| Kasai | River (basin) | native | 41591 |
| Kienke | River (basin) | native | 81639 |
| Komo | River (basin) | native | 81639 |
| Kouilou-Niari | River (basin) | native | 81639 |
| Kwango | River (basin) | native | 41590 |
| Lindi-Tshopo | River (basin) | native | 106290 |
| Loémé | River (basin) | native | 81639 |
| Lower Congo | River (basin) | native | 41591 |
| Lualaba | River (basin) | native | 93587 |
| Marine Lower Congo | River (basin) | native | 41591 |
| Mbini | River (basin) | native | 81639 |
| Middle Congo | River (basin) | native | 41590 |
| Mongala | River (basin) | native | 41590 |
| Muni | River (basin) | native | 81639 |
| Mweru | Lake | native | 45616 |
| Ndogo | River (basin) | native | 81639 |
| Nkomi | River (basin) | native | 81639 |
| Nyanga | River (basin) | native | 81639 |
| Nyong | River (basin) | native | 81639 |
| Ogowe | River (basin) | native | 81639 |
| Sanaga | River (basin) | native | 81639 |
| Sangha | River (basin) | native | 46233 |
| Uélé | River (basin) | native | 41590 |
| Upper Lualaba | River (basin) | native | 41590 |
| Wagenia Falls | River (basin) | native | 106245 |