In 1861, Gwynn received a commission for his service in the construction of the batteries at Charleston Harbor. He received command of the state defenses of Norfolk with a commission as a brigadier general. After this position expired, he took control of the coastal defenses in North Carolina. After the volunteers were disbanded in August 1861, he was granted the rank of colonel, and he served as a surveyor of the North Carolina coastal defenses until the end of the war.
