Reassigned to the North Atlantic Blockading Squadron, the monitor arrived at Beaufort, North Carolina, accompanied by the sidewheel gunboat , on 15 December 1864, and took part in the attacks on Fort Fisher, North Carolina. In the first engagement on 24–25 December, "Canonicus" anchored at ranges from and fired 144 rounds, Lieutenant Commander George Belknap claiming to have dismounted two Confederate guns. The ship was hit four times, but suffered no casualties and no significant damage. On 13–15 January 1865, during the second attack, "Canonicus" fired 279 shells at the fort, most on the first day, again claiming to have dismounted two guns. She was hit at least 38 times in return but was only lightly damaged, and three crewmen were wounded. The ship's flag was twice shot away and replaced each time by Quartermaster Daniel D. Stevens. Stevens was later awarded the Medal of Honor for his actions.