At the outbreak of the American Civil War Smith commanded the and on June 9, 1861, he captured the British blockade runner "Perthshire" with cargo of cotton near Pensacola, Florida. He also took part in the battles for Forts Jackson and St. Philip in April 1862. He was appointed captain and took part in the naval part of the Siege of Port Hudson in May to July, 1863. Smith was senior naval officer of a small fleet in Albemarle Sound where he attacked the Confederate ram at the Battle of Albemarle Sound in May 1864.