USS Conestoga was originally a civilian side-wheel towboat built at Brownsville, Pennsylvania, in 1859.

Conestoga's first combat action took place in September 1861, when she engaged CSS Jackson near Lucas Bend, Kentucky.

In February, she participated in an expedition up the Tennessee River that led to the capture of Forts Henry and Donelson.

She took part in the bombardment of Saint Charles, Arkansas, in June 1862 and was formally transferred to the navy in October of that year.

In April and July 1863, she was involved in expeditions to Palmyra, Tennessee, and up the Red River, Louisiana.