Promoted to commander on 17 November 1862, Colhoun took command of the steamer in the North Atlantic Blockading Squadron in 1863. Later that year, he became commanding officer of the monitor in the South Atlantic Blockading Squadron, and led "Weehawken" in various actions against Confederate forts – among them Fort Sumter, Fort Wagner, and Fort Beauregard – between 10 July and 15 September 1863. He next commanded the monitor from 1864 to 1865, engaging Howlett's Battery on the James River in Virginia on 21 June and 5 December 1864 and taking her into action in North Carolina in both the First Battle of Fort Fisher in December 1864 and the Second Battle of Fort Fisher in January 1865. He was commended for his participation in the bombardment and capture of Fort Fisher.