She was deployed in the York and James Rivers, Virginia, and performed service in support of Major General George B. McClellan's Peninsular Campaign of spring, 1862.

This squadron of seven vessels was deployed in the West Indies with orders to search for the destructive and elusive Confederate commerce raiders CSS Alabama and Florida.

On 18 January 1863, Wachusett and USS Sonoma captured the Southern merchant steamer Virginia off Isla Mujeres and took the British blockade runner Dolphin between Puerto Rico and St. Thomas Island on 25 March.

In the early morning darkness of the 7th, Wachusett got underway, steamed past the Brazilian gunboat anchored between his ship and Florida, and rammed the raider on her starboard quarter.

After undergoing repairs at the Boston Navy Yard, Wachusett, under its new captain, Commander Robert Townsend, got underway on 5 March 1865 and sailed, via the Cape of Good Hope, for the East Indies.

The executive officer John Woodward (Jack) Philip, (later Admiral) assumed command of the Wachusett and sailed it downriver with the goal of making it to Japan for the health of the crew.

She remained in Chinese waters into 1867, when under Captain Robert W. Schufeldt she attempted to enter Korea in order to investigate the demise of the USS General Sherman.

She sailed for the Gulf of Mexico on 5 June and visited New Orleans, Louisiana, and Vicksburg, Mississippi, to enlist seamen before returning to Boston in August.

[3] Wachusett, with Alfred Thayer Mahan in command, was stationed at Callao, Peru, protecting American interests during the final stages of the War of the Pacific.

[4][5] The vessel remained on the Pacific Station, cruising extensively until September 1885 when she was decommissioned at the Mare Island Navy Yard, Vallejo, California.