Control of Port Royal Sound enabled the Union Navy to coordinate the blockade of the southern Atlantic seacoast more effectively for the duration of the war.

On 10 November, Lt. Collins in Unadilla assumed command of Union naval forces off Beaufort, South Carolina, for the purpose of restoring order to the town following its capture two days before.

Unadilla delivered the schooner's two passengers to the authorities and sent the vessel north to the New York prize court; then on 20 and 21 May, she joined Pembina, Ottawa, and the surveying steamer Bibb in Stono Inlet, South Carolina, where the Union flotilla captured six armed Confederates.

There, during an exploratory expedition up the Ogeechee River on 29 July, Unadilla, Huron, and Madgie exchanged heavy gunfire with Confederate Fort McAllister for over an hour before retiring down the stream.

On 4 August, while patrolling between the Ogeechee and Vernon rivers in Ossabow Sound, Unadilla captured the British blockade-running steamer Lodona and her cargo of foodstuffs, dry goods, and building materials.

Princess Royal proved to be a rich catch, as she was laden with rifled guns, small arms, ammunition, and two powerful steam engines intended for ironclads.

In addition to routine patrol duties, Commodore McDonough, Unadilla and Pawnee entered the Kiawah River, South Carolina, on 28 February to ascertain if it were possible for the Confederates to install batteries on John's Island, but found that it was not.

There, the gunboat served with the reserve force during Rear Admiral Du Font's monitor attack upon the strong Confederate forts in Charleston harbor on 7 April.

After striking a sand bar, Unadilla returned to Port Royal in May where carpenters discovered that the battle-weary vessel needed an extensive overhaul.

Repairs completed, Unadilla departed Philadelphia, Pennsylvania, on 22 October, bound for Hampton Roads, Virginia, and duty with Rear Admiral David Dixon Porter's North Atlantic Blockading Squadron.

On 23 February, she was ordered to proceed to Hampton Roads and served in the James River, Virginia, squadron doing routine reconnaissance work until the end of the war.