When the Union Army moved into Northern Virginia on May 24, 1861, Barnard oversaw the erection of fortifications on the Arlington hills. He also accompanied the Army to Manassas in July 1861 and was present at the Union defeat at the First Battle of Bull Run (Manassas). Between June 1861 and September 1861, Barnard also served on the U.S. Navy's Blockade Strategy Board. Major General George B. McClellan assumed command of the Military Division of the Potomac, the troops around Washington, D.C., on July 23, 1861. On August 15, 1861, McClellan was appointed to the command of the Army and Department of the Potomac, and Barnard became chief engineer of the Military District of Washington. As McClellan formulated his thoughts for fortifications around Washington, D.C., Barnard planned, designed and oversaw their construction.