She was used by the Navy to patrol navigable waterways of the Confederate States of America, especially the Mississippi River, and to be employed as a gunboat when required.

While the other gunboats bombarded Fort Hindman, Rattler closed within 50 yards of the Confederate guns in an unsuccessful effort to clear away a barrier of chevaux-de-frise and was forced by heavy fire to return to station.

Rattler next served as flagship of a flotilla of "tinclads" and Army transports carrying 6,000 men of General Sherman's Corps during the Yazoo Pass expedition, an abortive attempt to bypass and isolate Vicksburg by means of bayous.

On 13 September 1863, Rattler's commanding officer, Acting Master E. H. Fentress, and 16 crewmen were captured by Rebel guerrillas while attending church at Rodney.

On 30 December 1864, during a heavy gale near Grand Gulf, Mississippi, Rattler's anchor cable parted and she was driven ashore, struck a snag, and sank.