| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Adriatic Sea | Sea/Bay/Gulf | native | 82476 |
| Aegean Sea | Sea/Bay/Gulf | native | 113897 |
| Atlantic Ocean | Sea/Bay/Gulf | native | 3397 |
| Balearic basins | River (basin) | extirpated | 59043 |
| Balearic Islands | Sea/Bay/Gulf | native | 95727 |
| Balkan river drainages and lakes | River (basin) | extirpated | 59043 |
| Baltic Sea | Sea/Bay/Gulf | native | 36252 |
| Bay of Biscay river drainages and lakes | River (basin) | extirpated | 59043 |
| Black Sea | Sea/Bay/Gulf | native | 4645 |
| British islands basins | River (basin) | extirpated | 59043 |
| Canary Current | Sea/Bay/Gulf | native | 3397 |
| Celtic-Biscay Shelf | Sea/Bay/Gulf | native | 35388 |
| Central Turkey river drainages and lakes | River (basin) | extirpated | 59043 |
| Corsica basins | River (basin) | extirpated | 59043 |
| Corsica Island | Sea/Bay/Gulf | native | 96325 |
| Cote Azur | River (basin) | extirpated | 59043 |
| Crete Island | Sea/Bay/Gulf | native | 113897 |
| Danish islands basins | River (basin) | extirpated | 59043 |
| Denmark river drainages and lakes | River (basin) | extirpated | 59043 |
| Dordogne | River (basin) | native | 51346 |
| Douro | River (basin) | extirpated | 59043 |
| Eastern Black Sea | River (basin) | extirpated | 59043 |
| Eastern Mediterranean river drainages and lakes | River (basin) | extirpated | 59043 |
| Elbe River | River (basin) | extirpated | 54732 |
| Evvoikos Gulf | Sea/Bay/Gulf | native | 113897 |
| Faroe islands basins | River (basin) | extirpated | 59043 |
| Garonne | River (basin) | native | 51346 |
| Garonne | River (basin) | native | 59043 |
| Greek islands basins | River (basin) | extirpated | 59043 |
| Iberian Coastal | Sea/Bay/Gulf | native | 35388 |
| Iberian main basins | River (basin) | extirpated | 59043 |
| Iceland river drainages and lakes | River (basin) | extirpated | 59043 |
| Ionian Sea | Sea/Bay/Gulf | native | 113897 |
| Ireland river drainages and lakes | River (basin) | extirpated | 59043 |
| Irish Sea | Sea/Bay/Gulf | native | 3193 |
| Italy main basins | River (basin) | extirpated | 59043 |
| Loire | River (basin) | native | 2196 |
| Mediterranean Sea | Sea/Bay/Gulf | native | 4645 |
| North Aegean | Sea/Bay/Gulf | native | 113897 |
| North Sea | Sea/Bay/Gulf | native | 4645 |
| Northern Atlanto-Baltic river drainages and lakes | River (basin) | extirpated | 59043 |
| Norwegian Sea | Sea/Bay/Gulf | native | 4645 |
| Palearctic | Zoogeographic realm | endemic | 3397 |
| Rhine | River (basin) | extirpated | 59043 |
| Rhône | River (basin) | extirpated | 59043 |
| Sakarya Nehri | River (basin) | extirpated | 59043 |
| Sardinia basins | River (basin) | extirpated | 59043 |
| Sardinia Island | Sea/Bay/Gulf | native | 13729 |
| Sea of Marmara | Sea/Bay/Gulf | native | 57855 |
| Seine | River (basin) | extirpated | 59043 |
| Sicily basins | River (basin) | extirpated | 59043 |
| Sicily Island | Sea/Bay/Gulf | native | 13729 |
| South Aegean | Sea/Bay/Gulf | native | 113897 |
| Weser | River (basin) | extirpated | 59043 |
| Yenice Irmagi | River (basin) | extirpated | 59043 |