"Powhatan" operated off Charleston, South Carolina from October 1862 to August 1863, captured schooner "Major E. Willis" on 19 April and sloop "C. Routereau" on 16 May, and deployed for a second time to the West Indies from November 1863 to September 1864 as flagship of Rear Admiral James L. Lardner. She participated in the successful reduction of Fort Fisher, 24–25 December 1864 and in its capture on 13–15 January 1865.