Hartford served in several prominent campaigns in the American Civil War as the flagship of David G. Farragut, most notably the Battle of Mobile Bay in 1864.

She departed the Delaware Capes on 28 January as flagship of Flag Officer David G. Farragut, the commander of the newly created West Gulf Blockading Squadron.

"Other operations," Secretary of the Navy Gideon Welles warned Farragut, "must not be allowed to interfere with the great object in view—the certain capture of the city of New Orleans.

Several Union ships and a few Army units were already in the vicinity when the squadron's flagship dropped anchor at the advanced staging area for the attack on New Orleans.

A line of hulks connected by strong barrier chains, six ships of the Confederate Navy—including ironclad Manassas and unfinished but potentially deadly ironclad Louisiana, two ships of the Louisiana Navy, a group of converted river steamers called the Confederate River Defense Fleet, and a number of fire rafts also stood between Farragut and the great Southern metropolis.

[2] On 16 April, the Union ships moved up the river to a position below the forts, and David Dixon Porter's gunboats first exchanged fire with the Southern guns.

In the early hours of 24 April, a red lantern on Hartford's mizzen peak signaled the fleet to get underway and steam through the breach in the obstructions.

[2] Hartford dodged a run by ironclad ram Manassas; then, while attempting to avoid a fireraft, grounded in the swift current near Fort St. Philip.

When the burning barge was shoved alongside the flagship, only Farragut's leadership and the training of the crew saved Hartford from being destroyed by flames which at one point engulfed a large portion of the ship.

[2] When Farragut's ships had run the gantlet and passed out of range of the fort's guns, the Confederate River Defense Fleet attempted to stop their progress.

[2] Orders awaited Farragut at New Orleans, where he arrived on 30 May, directing him to open the river and join the Western Flotilla and stating that Abraham Lincoln himself had given the task highest priority.

Two days later the Union ships, their own guns blazing at rapid fire and covered by an intense barrage from the mortars, suffered little damage while running past the batteries.

[2] Porter's Mississippi Squadron, cloaked by night, dashed downstream past the Vicksburg batteries on 16 April, while General Ulysses S. Grant marched his troops overland to a new base also below the Southern stronghold.

April closed with the Navy ferrying Grant's troops across the river to Bruinsburg whence they encircled Vicksburg and forced the beleaguered fortress to surrender on 4 July.

[8] In 1882, as Captain Stephen B. Luce's flagship of the North Atlantic Station, Hartford visited the Caroline Island, Hawaii, and Valparaíso, Chile, before arriving San Francisco on 17 March 1884.

President Franklin Roosevelt wanted to build a naval museum there featuring the Hartford, USS Olympia, and a four-stack destroyer from World War I.