In the winter of 1860-61 pro-Confederate sentiment was strong in Baltimore. Norris made no secret of his southern sympathies and with the outbreak of war he and his family left for Virginia. There he volunteered as a civilian aide on the staff of Brigadier General John Bankhead Magruder.
After Magruder sent Norris to learn signals in Norfolk under Captain Milligan,Milligan gave Norris a book of his system of signals and On July 18. 1861, Magruder gave Norris authority to establish a system of signals on the Peninsula and across the James River . Norris set up a network which employed flags and colored balls raised on poles. Due to his efforts on the signal system Norris was commissioned as a captain.
Norris also commanded the Secret Service Bureau, a unit within the Signal Corps. The Secret Service Bureau oversaw a communications network whose missions included the running of agents to and from Union territory and the forwarding of messages from Confederate officials in Richmond to contacts in Canada and Europe.
William Norris finally achieved the rank of colonel on April 26, 1865 and became the Commissioner of Exchange (of prisoners of war) replacing Colonel Robert Ould. Within a week Norris was in Union hands. Norris was held in detention in Richmond but eventually cleared of charge. On June 30, 1865 Norris swore allegiance to the United States.