The 21st Texas Cavalry saw action in the Trans-Mississippi Theater. As a lieutenant, Walton led scouting raids in the vicinity of Helena, Arkansas. In the spring of 1863, he commanded Maj. Gen. John S. Marmaduke's vanguard in the Battle of Cape Girardeau. Walton was later promoted to major and attached to the staff of Lt. Gen. Theophilus H. Holmes, commander of the Trans-Mississippi Department, and stationed at Little Rock, Arkansas. After the Battle of Helena and the Confederate evacuation of Little Rock, Walton took part in the Red River Campaign, leading a company in the battles of Pleasant Hill and Yellow Bayou. Walton's last assignment was with Brig. Gen. Alexander Watkins Terrell in southern Louisiana. Walton left the army without leave when he learned his wife was severely ill, following the birth of their daughter, Sarah, on October 24, 1864. He was never punished, because of the breakup of the Confederacy. In the final months of his life, Maj. Walton completed a manuscript of his experiences during the Civil War. He called it "The Epitome of my Life".