Assigned to the 11th district of the Mississippi Squadron, commanded by Lt. Mordeau Forrest, General Thomas served as a patrol vessel on the Tennessee River, above Muscle Shoals, Alabama.

At Decatur, Alabama, 28 October 1864, the gunboat engaged strong batteries from General John Bell Hood's army.

After passing the batteries downstream and sustaining several hits, General Thomas rounded to and, with Union Army gunboat Stone River, poured such a withering crossfire into the emplacements that the Confederates were forced to withdraw.

On 26 February 1865 she joined the other gunboats of the 11th district and, taking advantage of unusually high water, crossed Elk River Shoals.

This article incorporates text from the public domain Dictionary of American Naval Fighting Ships.