He took part in the Naval bombardment of Fort McAllister between January–March 1863 and although Union ships did not capture the fort, commanding admiral Samuel F. Du Pont had the opportunity to test ship's new guns. Ammen was relieved due to illness in June that year and was on sick leave until September. He was subsequently attached to the staff of the South Atlantic Blockading Squadron under Rear Admiral John A. Dahlgren and served as Dahlgren's aide aboard the USS "Philadelphia". Ammen took part in the Second Battle of Fort Sumter in September 1863.