| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Amudar'ya | River (basin) | native | 39701 |
| Aral Sea | Sea/Bay/Gulf | native | 683 |
| Atlantic Ocean | Sea/Bay/Gulf | native | 9696 |
| Balkan river drainages and lakes | River (basin) | native | 59043 |
| Balkanabat basin | River (basin) | native | 59043 |
| Baltic Sea | Sea/Bay/Gulf | native | 26334 |
| Bug | River (basin) | native | 59043 |
| Caspian Sea | Lake | native | 9953 |
| Central Danube | River (basin) | native | 59043 |
| Central Dnieper | River (basin) | native | 59043 |
| Central Don | River (basin) | native | 59043 |
| Danube | River (basin) | native | 59043 |
| Danube Delta | 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 |
| Don Delta | River (basin) | native | 59043 |
| Drava River | River (basin) | native | 59043 |
| Dwina | River (basin) | native | 59043 |
| Eastern Black Sea | River (basin) | native | 59043 |
| Eastern Caspian Sea river drainages and lakes | River (basin) | native | 59043 |
| Eastern Mediterranean river drainages and lakes | River (basin) | native | 59043 |
| Elbe River | River (basin) | native | 51031 |
| Goryn | River (basin) | native | 59043 |
| Issyk-Kul Lake | Lake | native | 41059 |
| Kama | River (basin) | native | 59043 |
| Khoper | River (basin) | native | 59043 |
| Krinka | River (basin) | native | 59043 |
| Kuban River | River (basin) | native | 58296 |
| Lower Danube | River (basin) | native | 59043 |
| Lower Dnieper | River (basin) | native | 59043 |
| Lower Prypiats | River (basin) | native | 59043 |
| Lower Volga | River (basin) | native | 59043 |
| Medvedista | River (basin) | native | 59043 |
| Neman (Niamunas) River | River (basin) | native | 59043 |
| North Sea | Sea/Bay/Gulf | native | 26334 |
| Northern Atlanto-Baltic river drainages and lakes | River (basin) | native | 59043 |
| Northern Caspian Sea river drainages and lakes | River (basin) | native | 59043 |
| Norwegian Sea | Sea/Bay/Gulf | native | 683 |
| Oder | River (basin) | native | 59043 |
| Onega River | River (basin) | native | 59043 |
| Palearctic | Zoogeographic realm | endemic | 9696 |
| Prut | River (basin) | native | 59043 |
| Psel | River (basin) | native | 59043 |
| Rhine | River (basin) | introduced | 30578 |
| Rud e Kal e Suhr | River (basin) | native | 59043 |
| Sakarya Nehri | River (basin) | native | 59043 |
| Sal | River (basin) | native | 59043 |
| Sarata | River (basin) | native | 59043 |
| Sava River | River (basin) | native | 59043 |
| Sea of Azov river drainages and lakes | River (basin) | native | 59043 |
| Severskiy Donets | River (basin) | native | 59043 |
| Siret | River (basin) | native | 59043 |
| Small Don Central | River (basin) | native | 59043 |
| Southern Baltic Coastal river drainages and lakes | River (basin) | native | 59043 |
| Southern Caspian Sea river drainages and lakes | River (basin) | native | 59043 |
| Syvash abo Gnyle more | River (basin) | native | 59043 |
| Terek 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 Don | River (basin) | native | 59043 |
| Upper Prypiats | River (basin) | native | 59043 |
| Upper Volga | River (basin) | native | 59043 |
| Ural | River (basin) | native | 59043 |
| Vistula | River (basin) | native | 59043 |
| Volga | River (basin) | native | 58297 |
| Volvi | Lake | native | 59043 |
| Weser | River (basin) | native | 59043 |
| Western Caspian Sea river drainages and lakes | River (basin) | native | 59043 |
| Yegorlyk-Manych | River (basin) | native | 59043 |
| Yenice Irmagi | River (basin) | native | 59043 |
| Yili River | River (basin) | introduced | 41093 |