"Canonicus" sailed from Boston on 22 April 1864 and arrived at Newport News, Virginia on 3 May for service with the James River Flotilla. She reached the mouth of the Appomattox River by 5 May. By 22 May, the ship was deployed with her sisters and "Tecumseh" on the James River where they protected the transports of Major General Benjamin Butler's Army of the James, supplying the army as it operated on the south bank of the river during the Bermuda Hundred Campaign. 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. The Confederates replied with a battery of four guns near the breastworks and "Saugus" and "Canonicus" joined in the bombardment. A half-hour later, Confederate ships near Dutch Gap joined in, but their fire was ineffective because they were firing blindly at the Union monitors. During the engagement, "Canonicus" fired forty 15-inch shells and was hit twice by Confederate shells. One shell pierced the upper part of the funnel and the other struck the deck and ricocheted into the turret; no one was wounded or killed during the engagement. The ship duelled with Howlett's Battery on 5 and 6 December, firing 46 shells without being hit in return. The only damage sustained was from the muzzle blast of the right gun that forced the armor at the gun port out about and broke a number of bolts.