She was used by the Union Navy as a gunboat assigned to patrol Confederate waterways to prevent the South from trading with other countries.

Assigned to the Mississippi Squadron, the new gunboat departed Cincinnati 2 July 1863 to patrol the Ohio River from Louisville, Kentucky, upstream.

Returning from Harpeth Shoals and escorting 10 transports to Nashville, Tennessee, Moose lay below Dover 9 November planning the destruction of a guerrilla camp near Palmyra, a mission carried out with Victory in December.

She joined USS Neosho 17 December to escort transports compelled to return to Nashville by a strong southern force.

Moose made a surprise attack on guerrillas crossing the Cumberland at Eddyville, Kentucky, 30 April 1865, completely dispersing and demoralizing the party.