Wright began constructing fortifications around Washington, D.C., before being assigned to the 3rd Division of the Department of Northeast Virginia under Maj. Gen. Samuel P. Heintzelman. Serving as Chief Engineer of the 3rd Division during the First Battle of Bull Run on July 21, 1861, Wright was promoted to major in August. Promoted to brigadier general of volunteers the following month, Wright was assigned as Chief Engineer to Maj. Gen. Thomas W. Sherman's November 1861 expedition against Port Royal, South Carolina. His successes while commanding Union troops in operations against Jacksonville, St. Augustine, and other military targets on the Florida coast from February to June 1862 led to his appointment as major general of volunteers and commander of the Department of the Ohio in August 1862, and commander of the newly created Army of the Ohio in March 1863. In this command he played a major logistical role in the repulse of Confederate General Braxton Bragg's invasion of Kentucky in 1862. His appointment as major general was not confirmed by the Senate and was revoked in March 1863. As a brigadier general, he was not considered eligible to command a department and Maj. Gen. Ambrose Burnside was sent to relieve him. Reporting to Burnside, Wright remained briefly as the commander of the District of Western Kentucky before returning to the East.