He served as a Union Army officer during the American Civil War and led the Wisconsin cavalry regiment which was credited in the capture of Confederate president Jefferson Davis.

He witnessed General Zachary Taylor land his army at Brazos Santiago and assisted ferrying wounded American soldiers back to New Orleans after the Battle of Palo Alto.

Harnden was promoted to sergeant, and then captain of Company L.[1] The regiment mustered into federal service in March 1862, and proceeded to St. Louis for operations in the western theater of the war.

[3] After receiving their equipment at Benton Barracks, they were sent down the Mississippi River to Cape Girardeau, Missouri, where their colonel, Edward Daniels, took command of the outpost.

By the end of September, the regiment was racked with disease, leaving 400 men sick and unable to travel at Cape Girardeau, Missouri.

The 1st Wisconsin Cavalry were among the defenders at the Battle of Cape Girardeau, holding out until relieved by Union reinforcements, then leading the pursuit of the enemy.

[3]: 889 After a few days rest, they joined the general pursuit of the rebel cavalry into Alabama, skirmishing for the next three months along the Tennessee–Alabama border associated with the Chattanooga campaign.

On May 3, 1864, the 1st Wisconsin Cavalry set off with the advance division on Sherman's Atlanta campaign, engaging in sharp skirmishing through northern Georgia.

At the Battle of Rocky Face Ridge, their colonel, Oscar Hugh La Grange, was captured by the enemy and several other officers were wounded.

Colonel Torrey went out sick and Major Paine was wounded, leaving Captain Harnden again in command of the regiment.

[3]: 892  Just a few days later, however, in the Battle of New Hope Church, Harnden led a charge against Confederate cavalry at Burnt Hickory and was also severely wounded when a pistol shot shattered his right arm.

[4] He spent most of the remainder of 1864 recuperating, but returned to his regiment around the time of the Battle of Nashville, and joined General James H. Wilson's pursuit of the Confederate forces under John Bell Hood into northern Alabama.

During the Battle of West Point, in which Colonel La Grange was in overall command of the Union force, Harnden led the detachment of Kentucky, Indiana, and Wisconsin cavalry which stormed and captured Fort Tyler.

Colonel Harnden to take a detachment of the 1st Wisconsin Cavalry to the east to attempt to cut off the escape of Confederate president Jefferson Davis.

Arriving at Dublin, Georgia, Harnden learned of a wagon train passing through the region which he believed to carry the Confederate president.

[3]: 897 Near Abbeville, Georgia, Harnden met with Colonel Benjamin D. Pritchard, whose 4th Michigan Cavalry Regiment was assigned to guard duty in the vicinity.

[3]: 899  President Andrew Johnson nominated Harnden for brevet to brigadier general on January 13, 1866, and the United States Senate confirmed the appointment on March 12, 1866.

One of his maternal uncles served aboard the USS Hornet and was wounded when it famously captured and sunk the British ship HMS Peacock in the War of 1812.