"[3] However, she suffered from further fitting-out delays and was not fully commissioned until May 18, 1864, almost a year later; she was made the flagship of the James River Squadron (replacing CSS Richmond in this role).

[4] Virginia II went into action on June 21, 1864, as the flagship of Commodore John K. Mitchell, during the engagement between the James River Squadron and Federal ships in Trent's Reach.

The Canonicus-class monitor, USS Saugus, and her gunboats joined in the battle, but could not effectively train their guns, though they did manage to fire two shots that hit Virginia II.

[7] From September 29 through October 1, the Virginia II and the rest of the squadron attacked New Market Heights and Fort Harrison in conjunction with the Confederate Army; it was the largest operation north of the James River since Cold Harbor and would remain so until the end of the war.

[8] In their routine patrol of the James River, the squadron was surprised to discover, on the morning of October 22, that the Union Army had finished fortifying Cox Hill.

[11] Her final action took place on January 23–24, 1865 when the James River Squadron, including ironclads Richmond, and Fredericksburg, with five smaller vessels, made a second unsuccessful attempt to circumvent obstructions in Trent's Reach.

After passing the Union batteries at Fort Brady sometime after 8 p.m., the Virginia II accidentally beached Torpedo by cutting too close to the shore.

Dawn came with most of the squadron in full view of the Union fortifications at Battery Parsons, and they had to suffer fire until the water rose high enough to allow them to finally retreat.

They suffered more heavy fire on their return upriver from Fort Brady, and Virginia II ran aground again before making it to the safety of Chaffin's Bluff.