He was promoted to master on 2 April 1852 and then to Lieutenant on 6 January 1853. From 1857 to 1859, he served as a division officer aboard during the sloop-of-war's tour as flagship of the U.S. Navy's Africa Squadron. In April 1862, Harrison commanded the gunboat at the Battle of Forts Jackson and St. Philip, leading the battle line past the forts and up the Mississippi River to New Orleans. He was promoted to Commander on 16 July 1862. He later commanded the gunboat in the James River Flotilla, the frigate in the North Atlantic Blockading Squadron and various ships in the South Atlantic Blockading Squadron. After the fall of Charleston in 1865, he served at the Portsmouth Navy Yard, Kittery, Maine.