British (and Allied) submarines played no direct part in the Dunkirk evacuation; the evacuation was carried out entirely by surface craft. Instead, they continued to carry out the same task they had been doing for much of the war, patrolling the North Sea to catch German shipping moving through the area. This did indirectly help the Dunkirk evacuation. By providing the Allies with early warning of any attempt by the German surface fleet to sortie and attack the evacuation, it let Allied commanders send more ships, especially the fast destroyers which carried a significant proportion of those evacuated, without having to worry about retaining them for a fleet action.

The German U-boat force took a more active role, forming part of the Kriegsmarine's response to the evacuation. Eight U-boats had been deployed to patrol the North Sea during the later half of May 1940. These boats would be sent into the Channel to supplement the motor torpedo boats (S-Boats), aircraft and coastal guns that were trying to stop the evacuation. They would see only one success, though. During the night of the 29-30th May, U-62 would be moving into position to attack Allied shipping on Route Y, the easternmost of the three routes used by shipping during the evacuation. Shortly after 2:30 AM, one of the ships on the route exploded. This was the British destroyer Wakeful, torpedoed by the S-boat S-30. Several ships stopped to render assistance, lowering boats and nets to rescue survivors from the water. This made them a prime target for U-62, which, at 2:50 AM, put a torpedo into the largest of the stopped ships; this was another British destroyer, HMS Grafton. She was set on fire, and began to slowly sink. As dawn broke, she was scuttled by gunfire from HMS Ivanhoe. While some of the surrounding ships attempted to rescue survivors from Grafton, others began hunting from the U-boat. While the submarine was not sighted, the crew of HMS Lydd mistook the British trawler Comfort for the attacker, and sank her with gunfire and by ramming.