One month following the outbreak of the War, Ammen was attached to the frigate USS "Roanoke" and immediately embarked for the Union blockade. He was aboard, when "Roanoke" destroyed the Confederate schooner "Mary" off Lockwood Folly Inlet, North Carolina, in July 1861. Ammen was appointed commanding officer of newly commissioned gunboat USS "Seneca" in September that year and took part in the South Atlantic Blockading Squadron.