Lacking a powerful naval arm to challenge Federal forces afloat, the South resorted to guerrilla raids and cavalry forays against Union bases along the riverbanks and on supply ships which plied the rivers bringing Mr. Lincoln's soldiers food, clothing, ammunition, and the other necessities of war.

Aided by Union troops under Major General Ambrose Burnside, they chased Morgan for almost 500 miles before they caught up with him at Buffington Island on the 19th and captured about half of the invading force.

She operated along the Ohio from Louisville, Kentucky, to Madison, Indiana, watchful against guerrilla batteries as she patrolled the river and escorted transports and supply ships.

In the months that followed, she frequently engaged Confederate batteries which fired upon her from temporary positions along the riverbanks as she reconnoitered the upper Cumberland and supported Army operations in Tennessee which would ultimately culminate in General William Tecumseh Sherman's death thrust through Georgia to the sea.

On 11 April 1864, Reindeer became a dispatch vessel for the Navy base at Mound City, Illinois, and served in that capacity until she decommissioned on 7 August 1865.