During the Civil War era, Fort Snelling served as an induction and training center for nearly twenty-five thousand soldiers. Many of them fought in the Civil War. Around fourteen hundred of the troops raised at the fort served in the US–Dakota War of 1862. After that war, a concentration camp for Dakota non-combatants was established near the fort. Following the Civil War, the fort supported US military expeditions against Indigenous people and the garrisoning of western posts.
When the Civil War began, Minnesota re-opened Fort Snelling as a training center for new recruits. The fort had several commandants throughout the period. The First Minnesota Volunteer Infantry Regiment was the first unit recruited at the fort in April of 1861.
While at the post, recruits learned the basics of soldiering. They spent the majority of their time marching, drilling with their weapons, and standing guard duty. After the draft began in 1863, several wooden barracks were built outside the fort's walls to accommodate the large number of new soldiers. At times, there were so many soldiers at the fort that some lived in tents.
Once a military unit's term of service ended, Fort Snelling served as its mustering-out point. In total, Minnesota recruited twenty-one military units during the Civil War, totaling about twenty-five thousand soldiers.
When the US–Dakota War began in August of 1862, a number of US regiments were being recruited at Fort Snelling. Colonel Henry Sibley assembled four infantry companies at the fort to march against the Dakota. Later, eight more companies and some mounted militia organized at the fort and joined Sibley at St. Peter.
When the US–Dakota War ended, about sixteen hundred Dakota and mixed-race non-combatants (mostly women, children, and the elderly) were removed to Fort Snelling. They were held in a concentration camp—a place where people are confined, often in poor conditions, without regard to legal norms of arrest—during the winter of 1862–1863 to await expulsion from the state. The camp was enclosed by a stockade and located on the river bottom below the fort in present-day Fort Snelling State Park.
According to eye-witness accounts, Dakota prisoners suffered assaults and violence at the hands of soldiers and white civilians. Conditions in the camp were poor. The Dakota lacked sufficient food. Outbreaks of mumps, measles, and pneumonia killed many. It is estimated that between 130 and three hundred Dakota died in the camp.
In April of 1863, a steamer carrying Dakota men who had been imprisoned at Mankato made a quick stop at Fort Snelling. US soldiers kept the Dakota men from reuniting with their families in the camp. The Dakota men were removed to a military prison in Davenport, Iowa, where the threat of mob violence was less. In May of 1863, the Dakota who had survived the winter in the concentration camp were removed to the Crow Creek Reservation. In addition, over two thousand Ho-Chunk (Winnebago) were briefly held at Fort Snelling before being removed from the state.
After the US-Dakota War, the Dakota leaders Sakpedan (Little Six; "Shakopee III"), and Wakanozhanzhan (Medicine Bottle) were imprisoned at Fort Snelling. A military commission convicted them of murdering civilians and participating in the war. Both men were executed at Fort Snelling on November 11, 1865.
From the summer of 1863 through 1866, troops mustered in and out of the Army at Fort Snelling. It also functioned as a supply base for operations against Dakota who had moved west. The army conducted three “punitive expeditions” into Dakota Territory that targeted Dakota who were deemed “hostile” by the US government. Soldiers recruited at Fort Snelling participated in all three expeditions.
The first two expeditions resulted in battles and attacks on American Indian villages. The vast majority of Indigenous people involved in these conflicts were Lakota and had not participated in the US–Dakota War. The final punitive expedition in 1865 failed to engage any Dakota. Many of the teamsters who served on the 1863 expedition were recently freed African American men. Many of them enlisted in the United States Colored Troops.
Until 1866, Minnesota troops garrisoned western posts. That year, Brackett’s Battalion of cavalry was the last Civil War-era unit to muster out of service at Fort Snelling.