Benton's propulsion system ultimately became her greatest failing. The vessel relied on a stern-mounted, steam-driven paddlewheel powered by two inclined engines. The configuration made the boat hardly agile and her turning radius was excessively wide, becoming and a time-consuming process to bring her bow about. Maximum speed in ideal conditions was 5.5 knots.
The vessel underwent her conversion at St. Louis, Missouri for service with the Western Gunboat Flotilla - interestingly of the United States Army and not Navy (the first three commanders of the Flotilla were in fact Navy men but fell under the direction of the Army). Benton was commissioned on February 24th, 1862 and was immediately put into action along the critical Mississippi River waterway and its many arteries. During this period, Benton took part in securing the surrenders of Island No. 10, Fort Pillow, and the city of Memphis, TN from the Confederates. She then faced off against CSS Arkansas near Vicksburg, MS and survived a ramming attempt before steaming up the Yazoo River a time later. During October of 1862, she was handed over to the U.S. Navy where she served as flagship (until 1863) of the Mississippi River Squadron with David Porter in command.
In operation along the Yazoo River once more during December of 1862, Benton took fire from Confederate guns and suffered damage but the vessel remained in service. In April of 1863, she managed to join several other Federal ships in bypassing the Confederate defenses at Vicksburg. She was then used to bombard the enemy stronghold at Grand Gulf, MS. In May, Benton used her guns in anger against Confederate positions at Fort DeRussy, AR and added firepower during the siege of Vicksburg - the strategically important river city fell on July 4th.
From March to May of 1864, USS Benton served in the Red River Campaign on Louisiana waters, marking her last notable actions in the American Civil War. With the war officially marked as over on May 9th, 1865, Benton returned to Louisiana waters in June to complete her service.
On July 20th, 1865 Benton was formally decommissioned which led to her sale on November 29th - ending her days as a naval fighting warship.
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