In 1853, Flandrau relocated to
Traverse des Sioux, Minnesota, to practice law. During the 1850s, he served on the Minnesota Territorial Council, in the Minnesota Constitutional Convention, and on the Minnesota territorial and state supreme courts. He was also appointed as U.S. Agent for the
Sioux in 1856; in this region they were
Dakota people. When the
American Civil War began, Flandrau was a vocal opponent. He refused to join the Union Army for any purpose of aggression against the
Confederates, damaging his credibility further. In August 1862, learning of a violent
Dakota uprising in the southwestern corner of the state (caused largely by the federal government's failure to deliver annuities in goods and payments on time, and resulting in the Dakota starving), Flandrau enlisted in the Union Army as a captain. He assembled an armed force and quickly went to the defense of settlers at
New Ulm. Both
Flandrau State Park and the community of
Flandreau, South Dakota, are named in his honor, as he was successful in defending the community.
Governor Alexander Ramsey appointed Flandrau in charge of the defense of the southwestern frontier of the state, and he served in this capacity at the rank of colonel for two years, simultaneous to his position on the Minnesota Supreme Court. In 1869 he ran for chief justice of the Minnesota Supreme Court, but was again defeated. In 1870, he moved to
St. Paul, Minnesota, where he began a legal partnership with Horace R. Bigelow and
Greenleaf Clark. He worked with them until his death in 1903. ==Personal life==