The vessel was assigned to the James River Flotilla of the North Atlantic Blockading Squadron upon completion in April 1864.

She engaged Confederate artillery batteries during the year and later participated in both attacks on Fort Fisher, defending the approaches to Wilmington, North Carolina, in December 1864 – January 1865.

Saugus returned to the James River after the capture of Fort Fisher and remained there until Richmond, Virginia, was occupied in early April.

A "rifle screen" of 1⁄2-inch (13 mm) armor 3 feet (0.9 m) high was installed on the top of the turret to protect the crew against Confederate snipers based on a suggestion by Commander Tunis A. M. Craven, captain of her sister ship Tecumseh.

On 21 June, Commander Craven of the Tecumseh spotted a line of breastworks that the Confederates were building at Howlett's Farm and his ship opened fire at the workers.

[11] Saugus was still under repair at the Norfolk Navy Yard in early September when she received orders to proceed with Canonicus and the gunboats Glaucus and Juniata 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.

After Butler ordered his men re-embarked onto their transports on 26 December, the monitor was towed to Beaufort, South Carolina, by the gunboat Quaker City.

Together with her sisters Canonicus and Mahopac, the double-turreted monitor Onondaga and the armored frigate New Ironsides, she bombarded the fort for three days until it was captured by Union troops.

Saugus was hit 11 times, cracking armor plates on her pilothouse and turret in addition to breaking bolts, but she was not badly damaged.

Nonetheless, the monitor was ordered to return to Norfolk for repairs on 16 January, towed by the sidewheel gunboat Rhode Island.

[6] Saugus remained on the James for the next month and contributed boats for clearing the river of "torpedoes" after the Confederate ships were scuttled on the night of 2/3 April and Richmond occupied.

[16] After the assassination of President Abraham Lincoln on 15 April, eight of the suspected conspirators were incarcerated aboard Saugus and the monitor Montauk.

After being towed to Philadelphia, Pennsylvania, for repairs, Saugus was recommissioned there on 9 November 1872 and was based at Key West until transferred to Port Royal, South Carolina in 1876.