Inkpaduta, a Mdewakanton Sioux Indian leader in the area from the 1850s until his departure to join Sitting Bull's band in Manitoba and Saskatchewan, camped at at the south end of the lake that gives the town its name both before and after his participation in the Spirit Lake massacre of 1857, and the Dakota War of 1862, also known as the Sioux uprising.
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Walter Mondale, Vice-President of the United States under Jimmy Carter (1977–1981) and the Democratic Party's nominee for President in 1984, attended Heron Lake Public High School and lived in the Methodist Episcopal Church parsonage (still present in the town) for three years prior to 1946.
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The first station out of Heron Lake was proposed in the extreme northeastern corner of Nobles County, and was originally named Warren, in honor of Joseph Warren who fell at the Battle of Bunker Hill.