| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 122734 |
| Congo | River (basin) | endemic | 54749 |
| Ethiopian | Zoogeographic realm | endemic | 3509 |
| Lindi-Tshopo | River (basin) | native | 122734 |
| Lomami | River (basin) | native | 54749 |
| Lower Congo | River (basin) | native | 54749 |
| Lualaba | River (basin) | native | 188 |
| Middle Congo | River (basin) | native | 54749 |
| Mongala | River (basin) | native | 54749 |
| Pool Malebo | Lake | native | 54749 |
| Ruki | River (basin) | native | 54749 |
| Sangha | River (basin) | native | 46233 |
| Tumba | Lake | native | 54749 |
| Ubangui | River (basin) | native | 54749 |
| Upper Lualaba | River (basin) | native | 2970 |
| Wagenia Falls | River (basin) | native | 42480 |