Assigned to the South Atlantic blockade

Conemaugh sailed from Portsmouth on 19 July 1862, and arrived at Port Royal, South Carolina on 30 July to join the South Atlantic Blockading Squadron. She patrolled and served as a picket frequently engaging Confederate batteries and detachments of troops along stream banks. Among such exchanges were those with the Cat Island battery on 5 March, 13 April and 23 May 1863 and Fort Wagner on 11 July-12 July. Conemaugh entered Philadelphia Navy Yard on 19 September and was placed out of commission four days later for overhaul.

Assigned to the West Gulf blockade

Clearing Philadelphia, Pennsylvania on 24 January 1864, Conemaugh arrived at Key West on 1 February for duty with the West Gulf Blockading Squadron. She carried stores and ordnance to the ships off Mobile, Alabama. She captured the blockade runner Judson on 30 April and sent her into Ship Island with her valuable cargo of cotton and turpentine.

With Admiral David Farragut's fleet, Conemaugh landed troops on Dauphin Island on 3 August and participated in the celebrated Battle of Mobile Bay on 5 August. She sailed from Key West on 5 November for overhaul at Philadelphia.

Reassigned to the South Atlantic blockade

From 20 May-22 November 1865, Conemaugh cruised the coast of North and South Carolina with the South Atlantic Blockading Squadron. She lay at Norfolk, Virginia from 25 November 1865 – 27 May 1866, then was assigned to the North Atlantic Squadron.