Promoted to captain he took part in the attack on Port Royal by the fleet under Admiral Samuel Francis Du Pont. He placed in position to secure an enfilading fire on the fort on Hilton Head, and materially assisted in silencing the batteries of the enemy. In 1863 he was promoted to commodore; and commanded the 4th Division of Admiral David Dixon Porter's fleet at the first and second battles of Fort Fisher, North Carolina, in December 1864 and January 1865. In the report of the latter action he was specially commended for the support rendered the commander-in-chief, and for the good discipline and accurate firing of his ship, the .