The next morning, she resumed firing in company with USS Underwriter (1852) and other Federal warships as they started to pass a cluster of vessels which had been sunk as obstructions.

Although running aground at one point during the fight and suffering a hit on the hurricane deck, William G. Putnam emerged with no casualties from the heavy shelling by enemy guns.

In the operation, Union warships captured the CSS Ellis; obstructed the passage to the Albemarle and Chesapeake Canal; and raised the stars and stripes over Cobb Point battery.

Needing repairs, William G. Putnam, sailed for Hampton Roads and arrived there on 22 October with intelligence data for Rear Admiral Samuel P. Lee.

Ordered to capture or destroy all Confederate vessels that could be used to run the Union blockade, William G. Putnam carried out her assignment until the successful completion of the campaign against Mathews Court House on 23 November 1862.

Subsequently, serving as guard vessel in the York River and off neighboring coasts, the tug cooperated with the Union Army in landing troops on expeditions up to West Point, Virginia, and enforced the blockade by patrolling the region until 15 January 1863.

Nevertheless, William G. Putnam remained on active service in those waters, stationed so as to enfilade Gloucester Point, until towed to Baltimore, Maryland, to receive a new boiler and rifle screening.

Men from the steamers manned two cutters, two boats, and a gig and gave chase but soon encountered heavy sniper fire from Confederate soldiers and guerrillas in the woods.

William G. Putnam's commanding officer, Acting Master Hotchkiss, fell mortally wounded in the first enemy volley, and the boats withdrew while returning fire.

William G. Putnam remained on picket duty off the mouth of the Nansemond River to intercept blockade runners until 15 December, when she returned to Newport News.

Informed that Confederate pickets had advanced in force as far as Gilliam's Bar, the Union flotilla retreated on 11 May to Point of Rocks and shelled the nearby woods.

During the action, William G. Putnam discovered the Confederate battery at Fort Clifton, opened fire on enemy guns and soon obtained the range.

On 28 July 1864, Rear Admiral Lee assigned William G. Putnam to a division under the command of Captain Melancton Smith operating on the James River.