Commodore McDonough — an armed, side-wheel ferry — was purchased on 5 August 1862 in New York City; fitted out at New York Navy Yard; and commissioned on 24 November 1862, Lieutenant Commander G. Bacon in command.
Commodore McDonough joined the South Atlantic Blockading Squadron at Port Royal, South Carolina on 11 December 1862. Throughout her service, she operated in South Carolina waters, primarily off Charleston, but often cruising up the many rivers of that coast to bombard shore installations, cover the landing of troops, engage Confederate batteries, and perform reconnaissance. In the continuing operations in Charleston Harbor, she frequently bombarded the forts protecting the city.
At the close of the war, she assisted in harbor clearance at Port Royal, South Carolina, and on 23 August 1865 — while under tow for New York — she foundered.