The Kriegsmarine was largely a defeated and spent force by June 1944. The surface fleet had relocated largely to the safer harbors of the Baltic and Norwegian ports since the major heavy units had made the "Channel Dash" in early 1942. This left the submarines as the only real large combatants available to meet the Allied armada, and even here, German strategy had shifted. Allied air superiority and ASW had forced a reorientation of German naval strategy towards the North Sea and U-boat bases in Norway, which was a tacit admission of their defeat. The Norwegian bases were not subjected to the same umbrella of Allied air interdiction to the scale of their French-based counterparts. There were some U-boats still in operation in France, but as this map shows, they were on the wrong side of France to patrol and intercept the invasion flotilla.

The problem was by 1944, Allied air cover over the Bay of Biscay was so omnipresent that the general tactic of U-boats was to make a beeline out of the area once they went to sea. All of the Biscay-based U-boats could reach the Channel, but this was sailing into the maw of the dragon as Allied air cover became stronger the closer one got to the British Isles. It's important to realize that the typical German U-boat was not a true submersible; they could only crawl around on batteries underwater for a few hours. Their design was predicated upon long-range surface cruises using diesels and attacking underwater. Even then, wartime experience showed the German U-boats tended to be more successful making surface attacks, often at night. The Schnorkel (basically a periscope exhaust pipe) rectified some of these flaws, but they often degraded crew performance (they created uncomfortable changes in pressure, the U-boats relied upon surfacing to clear their "ballast"- i.e. human waste), situational awareness (periscopes and passive sonar), and were still visible to Allied radar.

The Kriegsmarine's defense of the Channel was focused primarily upon E-boats and specialized minisubmarines like the Marder and Neger that would attack after the invasion had begun. Neither of these light units could be expected to seriously damage the Allied flotillas. Although the E-boats were a battle-tested weapon, the minisubmarines were untested and combat experience would show that they were poorly suited for this type of war in the Channel muck. There were also some conventional U-boats that also attacked the invasion flotilla, but between June and August, the Kriegsmarine lost 15 U-boats in the Channel. The Kriegsmarine could not prevent the invasion, nor did it have the capabilities to damage the armada in a significant fashion.