At the outbreak of the Civil War in April 1861, Wyman was a commander in the service of the United States. In September, Wyman assumed command of the Pocahontas, as part of the Potomac River Flotilla. However, he soon took command of the steamer Pawnee in October 1861. Wyman took part in Flag Officer DuPont's capture of the key seaport of Port Royal, S.C. After that operation, Wyman returned north and took command of the Potomac River Flotilla in December 1861. As commander of this flotilla, he led the Union forces in the Battle of Cockpit Point, in January 1862. .He held this post until the end of June 1862. During his time in the Potomac, he was active in maintaining Union control of that vital river and of much of the Rappahannock during the Peninsula Campaign.
Promoted to commander on 16 July 1862, Wyman was ordered to command the gunboat Sonoma on the James River. Transferred to the West Indian Squadron the following October, he commanded the steam sloop Wachusett and the paddle steamer Santiago de Cuba, and captured the blockade runners Brittania and Lizzie. During the last two years of the war, he served on special duty in the Navy Department in Washington.
