Winnebago County took its name from the American Indian tribe that had formerly lived in this vicinity. The word was an Algonquian term applied to the Siouan tribe, and signified, "people dwelling by the fetid or ill-smelling water" (possibly a sulphur spring) -- see Wis. Hist. Colls., xvi, p. 3; Thwaites, Wisconsin (Boston, 1908), pp. 16, 17.  Another interpretation suggests the tribe came from the ocean--and American Indians considered salt water "unclean".

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[Source: Kellogg, Louise Phelps. "Derivation of County Names" in Proceedings of the State Historical Society of Wisconsin for 1909, pages 219-231; Milwaukee Sentinel, June 29, 1953.]