Promoted to the rank of captain in July 1862, he commanded the steam sloop Housatonic during the next several months. In 1863, he was Fleet Captain of the South Atlantic Blockading Squadron. In that role, he participated in attacks on Confederate fortifications protecting Charleston, South Carolina. Captain Taylor commanded the steam sloop Juniata during 1864–65 and took part in the operations that led to the capture of Fort Fisher, North Carolina.
In 1866, a year after the end of the Civil War, Taylor was advanced to the rank of Commodore. For the next five years, he had further ordnance duty and commanded the Northern squadron of the Pacific Fleet. He reached the rank of Rear Admiral in early 1871 and spent his final active duty period as President of the Board of Examiners. Rear Admiral William Rogers Taylor was placed on the Retired List in November 1873. He died at Washington, D.C., on 14 April 1889.