With a crew of 112 sailors, she was employed by the Union Navy as a heavy gunboat outfitted to pursue blockade runners of the Confederate States of America, and to participate in river operations.

Four days later, two boats from Shokokon destroyed schooner, Alexander Cooper, in New Topsail Inlet, North Carolina, and demolished extensive salt works in the vicinity.

She returned to Newport News on the morning of 16 January 1864 and, for the remainder of the war, was active in supporting Union ground forces in the rivers of Virginia and North Carolina.

On 5 May, she was one of the warships which swept the river to clear away Confederate torpedoes (naval mines) and then supported the crossing of the landings at Bermuda Hundred and City Point, Virginia, which established a Union bridgehead on the southern shore of the James.

During the ensuing months, she continued to shuttle between the York and James rivers to assist ground operations in General Ulysses S. Grant's ever tightening stranglehold on Richmond.