In the course of the ensuing furious engagement, only Hartford and Albatross succeeded in passing upriver, Richmond losing her steam power early in the battle and drifting downstream out of range with Genesee lashed alongside.

Monongahela grounded under the guns of a heavy battery, taking a pounding and losing six men killed and 21 wounded, including the captain, until she worked loose with Kineo's aid.

On 27 May, Confederate defenders turned back a major assault on Port Hudson following constant bombardment by Monongahela, serving as temporary flagship of Admiral Farragut, and other ships of the squadron.

On July 7, the ship, in company with USS New London, engaged southern field batteries behind the levee, 12 mi (19 km) below Donaldsonville, Louisiana, Monongahela's new skipper Commander Abner Read being killed in this action.

While on service with the West Indies Squadron, the warship had the unique experience of being landed high and dry 91 meters inland from the shoreline when a tsunami struck Frederiksted, St. Croix on November 18, 1867.

Monongahela continued her duty in the Pacific Squadron as storeship at Callao, Peru in 1890, and then sailed around Cape Horn to Portsmouth Navy Yard to be fitted out as an apprentice training ship.

Finally detached from the Atlantic Training Squadron on May 9, 1904, the old warship served as a storeship at Guantanamo Bay, Cuba until totally destroyed by fire on March 17, 1908.