The land invasion of the Soviet Union and its general tactics and plans have been covered very much in detail. But my question regards the Soviet Navy and how the Nazis thought to deal with it. Both the northern and southern section of Barbarossa covers a number of big port cities, like Riga, Odessa, even Leningrad if they manage to reach it. If not at anchor at the time, they’re essential supply ports for the Soviet Navy and would be vulnerable to recapture by sea assault. So what was the Nazi plan to deal with the Soviet Navy during Barbarossa?
I can only tell what i know of the Baltic Sea. And to be clear I do not know exact German plans. What the Germans believed was that once cornered in collapsing Leningrad the Soviet Baltic Fleet would try to escape and avoid capture when the last ports would fall. This was one of the reasons for the extensive minefields in the Baltic Sea - to prevent the Soviet Fleet from sailing to Sweden (to be interned there). Other goals had been to prevent the Soviets from otherwise breaking out from the end of the Gulf of FInland to the Baltic Sea and also to prevent the Soviet evacuations like for example from Tallinn and to lesser extent from Hanko.
The Germans also formed under the name of ‘Baltenflotte’ a rather remarkable number of ships from the ones they had available at the time: battleship Tirpitz, cruisers Admiral Scheer, Emden, Köln, Leipzig and Nürnberg, destroyers Z25, Z26, Z27 and the 2nd torpedo boat squadron. This force together with supporting light forces, submarines, minefields, and the Finnish navy was to destroy the Soviet Baltic Fleet when it would try to reach relative safety of Sweden. Formation was disbanded when it became apparent that the Soviet Baltic Fleet had been seriously damaged by bombs and shells (the major vessels that is).
As to sea assaults… Germans didn’t make all that many of them - and the lack of strong naval assets prevented those from being carried out directly against strongly defended targets. There was the https://en.wikipedia.org/wiki/Operation_Beowulf Operation Beowulf - a naval assault (though more like extended crossing) to capture islands of Saaremaa, Hiiumaa and Muhu (Ösel, Dagö, Mohn/Moon).