Reed Werden was on the steam frigate USS Minnesota when the Civil War began and participated in the attacks of the forts at Hatteras Inlet and operations in the North Carolina Sounds in Stringham's fleet. The USS Stars and Stripes, his former ship, was also there.
He commanded the steamers USS Yankee and USS Stars and Stripes in the North Atlantic Blockading Squadron 1861-1862. While in command of the Stars and Stripes, he led the First Division in the capture of Roanoke Island, North Carolina.
He was commissioned to the rank of commander 16 July 1862, and commanded the USS Conemaugh in the South Atlantic Blockading Squadron 1862-1863.