In September 1861, during the Civil War, Lardner, in command of the frigate , took a pertinent part in the Battle of Port Royal and the capture of Forts Walker and Beauregard. He was commended for gallantry in action by Rear Admiral Samuel F. Du Pont; his name was sent to Congress for a vote of thanks by President Abraham Lincoln. In May 1862, he assumed command of the East Gulf Blockading Squadron and was promoted to commodore on July 16, 1862. In December 1862 he returned to Philadelphia to recover from a severe attack of yellow fever. From May 1863 to October 1864, Lardner commanded the West India Squadron.