In November 1861, Confederate troops began to build a defensive fort that would control the river approach to Clarksville. They mounted three guns in the fort. On February 19, 1862, Federal gunboats came up the river from Fort Donelson and reported the fort displayed a white flag and was deserted. The Federals took over the fort and enlarged it so that it would control traffic on the Hopkinsville Pike. Clarksville was left with a small garrison of Union Troops. In April 1862, this small garrison was made up of the 71st Ohio Volunteers commanded by Col. Rodney Mason.
During July and August 1862, there was an increase in guerrilla activity around Clarksville. On August 18, 1862, Clarksville was recapturered by Confederate Calvary. Col. Mason was cashiered for surrendering Clarksville so easily. Union soldiers were sent from Fort Donelson to retake Clarksville in September 1862. Skirmishes were fought at New Providence on September 6, 1862 and at Riggins Hill on September 7, 1862. The town and fort were reoccupied by Federal troops who remained for the rest of the war. Col. Bruce was placed in command at Clarksville and Fort Defiance was renamed Fort Bruce.
At one point in time, Fort Defiance was also referred to as Fort Sevier.