When war erupted in early 1861, Potter was still stationed in Texas. He was captured by Confederates at St. Augustine Springs on July 27, 1861, and was held as a prisoner of war for more than a year. He was finally exchanged on August 2, 1862. He returned to active duty and was assigned command of the 12th New Hampshire Infantry as a colonel in the volunteer Union Army while retaining his rank of captain in the Regular Army.
