At the outbreak of the Civil War, Walton and four of five batteries went East to serve in Virginia. After fighting at the First Battle of Manassas, Walton and his command were assigned to James Longstreet's forces. These batteries served in the Peninsula Campaign, at Second Manassas, and Antietam. Walton commanded the batteries on Marye's Heights during the Battle of Fredericksburg and the Chancellorsville Campaign. He commanded the artillery reserve of the First Corps artillery and was offended when at Gettysburg a subordinate Colonel E. Porter Alexander was placed in charge of the artillery preparation for Pickett's Charge on July 3, 1863.