Renamed Noe-Daquy, she operated during the early months of the American Civil War and in December 1862 was acquired by merchant at Havana, Cuba, for use as a Confederate blockade runner.

However, further repairs and modifications were needed before she could become a fully effective fighting unit, and she spent August and most of September 1863 at New Orleans, Louisiana, undergoing overhaul.

There, she conducted numerous patrol and reconnaissance missions – which often took her up the rivers – and also compiled an impressive list of captures while enforcing the Union blockade of the Confederacy.

After the Rio Grande expedition, Virginia returned to blockade duty and found the waters off Texas a fertile breeding ground of smuggling activity.

Virginia′s last captures off San Luis Pass included the schooner Experiment, which she took on 3 May 1864 and subsequently destroyed, and 94 stacked bales of cotton picked up ashore on the 7 and 8 May 1864.

She also discovered the British sidewheel steamer Acadia wrecked on the coast of Texas about 6 miles 9 10 km) east-northeast of Velasco on 5–6 February 1865 and shelled her, but was unable to launch a boat crew to board and burn her because of rough seas.