At the outbreak of World War II, he was stationed on the battleship , participating in the Battle of Westerplatte and Battle of Hel. He transferred to the U-boat Arm in 1940, at first serving as a watch officer on before taking command of "U-68" in early 1941. Commanding "U-68" on five war patrols, patrolling in the Atlantic Ocean, the Caribbean Sea and the Indian Ocean, he was awarded Knight's Cross of the Iron Cross on 13 June 1942 and the Oak Leaves to his Knight's Cross on 16 November 1942. On the second patrol, Merten helped rescue the crews of the auxiliary cruiser "Atlantis" and the refuelling ship "Python", which had been sunk by the Royal Navy. In January 1943 Merten became the commander of the 26th U-boat Flotilla and in March 1943, Merten was given command of the 24th U-boat Flotilla. In February 1945, he was posted to the "Führer" Headquarters in Berlin. At the end of the war, he was taken prisoner of war by US forces and released again in late June 1945.