"Saugus" was still under repair at the Norfolk Navy Yard in early September when she received orders to proceed with "Canonicus" and the gunboats and to Port Royal, South Carolina, and there await Admiral David Farragut, the prospective commander of the North Atlantic Blockading Squadron, in anticipation of an attack on Fort Fisher. This deployment was cancelled on 19 September when poor health caused Farragut to decline the appointment. The ship returned to the James and resumed supporting the Union Army. In an engagement with Howlett's Battery on 5 December, "Saugus" was hit twice. One of the shots from a Brooke rifle disabled her turret temporarily when it cracked an armor plate and broke a number of bolts. The monitor ran aground on 14 December and she was refloated the following day. "Saugus" was repaired at Norfolk and she was then towed by the gunboat "Nereus". They departed on 22 December and arrived off Fort Fisher on Christmas Eve. The next day, "Saugus" joined the bombardment of the Confederate fortifications from a range of . Colhoun reported that he saw one Confederate gun dismounted by his ship's shells; "Saugus" fired 64 shells during the day. After Butler ordered his men re-embarked onto their transports on 26 December, the monitor was towed to Beaufort, South Carolina by the gunboat .