After Soviet evacuation of Tallinn, Kronstadt became the main base of the Soviet Baltic Fleet.
The Gulf of Finland is fairly narrow and shallow in the East (where Kronstadt is located),
...the Baltic Fleet was confined to the innermost part of the Gulf of Finland by German minefields...
Basically, the problem was that the only remaining Soviet naval base was in a spot which was relatively easy to isolate with mines, and, critically, the Germans enjoyed air superiority which enabled them to set the minefields almost unmolested.
If the Allies have placed all its Mediterranean naval forces in a "narrow gulf" and waited for the Axis to blockade them with minefields, they would have been in trouble too. However, the Allies had several bases (Gibraltar, Malta, Alexandria) which were relatively well protected from the air.