In 1861, Irwin reported for duty aboard the screw frigate . The American Civil War broke out in April 1861, and Irwin saw a great deal of action against Confederate forces aboard "Wabash". During Irwin's tour, "Wabash" participated in the capture of Forts Hatteras and Clark at Hatteras Inlet, North Carolina, on 29 August 1861, before becoming the flagship of the South Atlantic Blockading Squadron, one of the squadrons engaged in the Union blockade of Confederate ports. "Wabash" then took part in the capture of Fort Walker, Fort Beauregard, and Port Royal Sound, South Carolina, in the Battle of Port Royal on 7 November 1861. Irwin later was in command of boat howitzers "Wabash" placed ashore during the Battle of Port Royal Ferry, South Carolina, on 1 January 1862, and was aboard "Wabash" for the Battle of Fort Pulaski at Cockspur Island, Georgia, on 10–11 April 1862. He was promoted to lieutenant commander on 16 July 1862.