| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Balkan river drainages and lakes | River (basin) | native | 59043 |
| Bug | River (basin) | native | 59043 |
| Caspian Sea | Lake | native | 47532 |
| Central Danube | River (basin) | native | 59043 |
| Central Dnieper | River (basin) | native | 59043 |
| Danube | River (basin) | native | 59043 |
| Danube Delta | River (basin) | native | 59043 |
| Denmark river drainages and lakes | River (basin) | native | 59043 |
| Desna | River (basin) | native | 59043 |
| Dnester | River (basin) | native | 59043 |
| Dnieper-Bug Liman | River (basin) | native | 59043 |
| Don | River (basin) | native | 58293 |
| Drava River | River (basin) | native | 59043 |
| Drin River | River (basin) | native | 59043 |
| Eastern Mediterranean river drainages and lakes | River (basin) | native | 59043 |
| Elbe River | River (basin) | native | 59043 |
| Goryn | River (basin) | native | 59043 |
| Kuban River | River (basin) | questionable | 58296 |
| Lower Danube | River (basin) | native | 59043 |
| Lower Dnieper | River (basin) | native | 59043 |
| Lower Prypiats | River (basin) | native | 59043 |
| Marmara | Lake | native | 86351 |
| Oder | River (basin) | native | 59043 |
| Palearctic | Zoogeographic realm | endemic | 557 |
| Prut | River (basin) | native | 59043 |
| Psel | River (basin) | native | 59043 |
| Rhine | River (basin) | native | 59043 |
| Rhône | River (basin) | native | 59043 |
| Sakarya Nehri | River (basin) | native | 59043 |
| Sarata | River (basin) | native | 59043 |
| Sava River | River (basin) | native | 59043 |
| Seine | River (basin) | native | 2196 |
| Siret | River (basin) | native | 59043 |
| Southern Baltic Coastal river drainages and lakes | River (basin) | native | 59043 |
| Struma River | River (basin) | native | 59043 |
| Teterev | River (basin) | native | 59043 |
| Tisza | River (basin) | native | 59043 |
| Upper Danube | River (basin) | native | 59043 |
| Upper Dnieper | River (basin) | native | 59043 |
| Upper Prypiats | River (basin) | native | 59043 |
| Vistula | River (basin) | native | 59043 |
| Volga | River (basin) | native | 58297 |
| Weser | River (basin) | native | 59043 |