Operating under the name Upper Missouri Agency in 1861, the agency was renamed Crow Creek Agency in 1874. By 1871 the agency was located at Soldier Creek on the east bank of the Missouri River, about eight miles from present day Crow Creek.
The Lower Yanktonai were settled at Crow Creek Agency after the treaty of 1859 ceded all lands of the Yankton and Yanktonais to the federal government, a result of the Spirit Lake massacre.
After the 1862 uprising in Minnesota, members of the Lower Agency Mdewakanton and Wahpekute bands of Santee and Winnebago Indians were moved to Crow Creek. The Winnebagos were removed to the Omaha reservation in Nebraska in 1865. In 1866, after the arrival of several hundred Lower Yanktonai, Sicangu, and Oohenunpa, the Santee were removed to a separate reservation in Nebraska. The following year, the Sicangu and Oohenunpa settled on the west bank of the Missouri River across from the Crow Creek Agency at Lower Brule Agency.
Drifting Goose, leader of the Hunkpati band of Yanktonai, is remembered for refusing to sign the 1859 treaty. He was proud of the fact that he "signed nothing" and gave up "nothing." His scare tactics against non-Indians forced President Rutherford Hayes to set aside a 65,000-acre reservation along the James River for his Hunkpati band. A year later, in 1880, Drifting Goose and his people gave up their reservation and settled at Crow Creek Agency.
Today the reservation is located along the east bank of the Missouri River in central South Dakota in Hughes, Hyde, and Buffalo counties. The land base is 125,591 acres. Contemporary artist Oscar Howe (1915-1983) and writer Elizabeth Cook-Lynn are from Crow Creek Agency.