Valley City was reassigned to the North Atlantic Blockading Squadron under Flag Officer Louis M. Goldsborough in October but first put into the Baltimore Navy Yard, Maryland, for emergency repairs to her funnel.

Valley City remained off Hatteras Inlet for one month and then participated in the successful amphibious assault upon Roanoke Island, North Carolina, on 7 and 8 February.

In January 1863, the vessel returned to the Norfolk Navy Yard for a new propeller and underwent further repairs and alterations at Baltimore, Maryland, before deploying off Washington, D.C., in April.

Valley City sailed for Hampton Roads on 27 November and proceeded on to Baltimore for repairs and did not return to New Berne until 19 February 1864, when she resumed her now familiar patrol and reconnaissance activities.

During the summer months of May through September 1864, the steamer played an important role in support of Union forces ashore and afloat in scattered operations in the Roanoke, Chowan, Pamlico, Pungo, and Scuppernong rivers of North Carolina.

While on an expedition up the Roanoke River on 20 December, the vessel suffered two casualties in a surprise attack by hidden Confederate shore batteries at Poplar Point, North Carolina.

In May, USS Iosco, Valley City, and a picket boat captured a motley collection of small Confederate watercraft during a sweep of the Roanoke River and also dragged the bottom for sunken guns and unexploded torpedoes (mines).