| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Balkan river drainages and lakes | River (basin) | native | 59043 |
| Central Danube | River (basin) | native | 59043 |
| Danube | River (basin) | native | 56371 |
| Don | River (basin) | questionable | 58293 |
| Drava River | River (basin) | native | 84350 |
| Gallikos | River (basin) | native | 59043 |
| Kupa River | River (basin) | native | 84350 |
| Lower Danube | River (basin) | native | 59043 |
| Maritza | River (basin) | native | 59043 |
| Palearctic | Zoogeographic realm | endemic | 13696 |
| Petrinj?ica River | River (basin) | native | 84350 |
| Pinios | River (basin) | native | 59043 |
| Sava River | River (basin) | native | 84350 |
| Siret | River (basin) | native | 59043 |
| Tisza | River (basin) | native | 59043 |
| Una River | River (basin) | native | 84350 |
| Upper Danube | River (basin) | native | 59043 |
| Vardar | River (basin) | native | 59043 |
| Vo?inska River | River (basin) | native | 84350 |