Marion was powered by a 500 hp single-cylinder vertical beam steam engine with 38 inches (0.97 m) bore and 9 feet (2.7 m) stroke, built by the Novelty Iron Works of New York.

She lay off Newport News, Virginia, until 29 December when she steamed across Hampton Roads in an attempt to capture the CSS Sea Bird; Morse's shelling drove the steamer to the protection of three batteries at Sewell's Point.

On 9 February, Morse and USS Commodore Perry steamed up Croatan Sound for Elizabeth City, North Carolina, to destroy Confederate gunboats and break up canal communications.

Strong Confederate forces at Winton, North Carolina, opened heavy fire on USS Delaware, the lead ship, with artillery and musketry.

The ships returned the attack, firing on the battery and landing the 9th New York Zouaves, who entered Winton, destroying military stores, tents, arms, and gear.

After searching out torpedoes (mines) on Purtan Bay in February 1864, Morse joined General Wister's campaign on the Mattapony River, attacking King and Queen Courthouse.