After the start of the Civil War, Ayres was promoted to captain and commanded a battery in the 5th U.S. Artillery, which he led in the First Bull Run Campaign, and was heavily involved in the Battle of Blackburn's Ford, immediately before the larger First Battle of Bull Run. At First Bull Run, his battery, attached to the brigade of William Tecumseh Sherman, was held in reserve and he did not see action during the battle proper, but distinguished himself by providing cover for retreating Union Army troops pursued by Confederate cavalry.