The ferryboat departed New York City on 21 October, served briefly at Hampton Roads, Virginia, reached the Washington Navy Yard on 5 November, and was promptly placed in service as a dispatch boat in the Potomac Flotilla.

When assigned to the North Atlantic Blockading Squadron, the ship was moved from the James, to the York, or to the Rappahannock River as demanded by the military situation ashore.

Highlights of Stepping Stones' service were the operations on the James in July 1862 to help protect General George B. McClellan's beleaguered army at Harrison's Landing.

One notable event was rescuing, under heavy fire, of USS Mount Washington when that ship had been grounded and disabled during and engagement with an earth works near Suffolk, Virginia.

Later, after running the same battery, she made two landings against the earth works; which fell in an assault by Union Army units supported by the Stepping Stones' boat howitzers.