- Waukon is a city located in Allamakee County, Iowa, United States. It is the county seat of Allamakee County. According to the United States Census Bureau, the city has a total area of 6.50 square miles and a population of approximately 3,800 people. Waukon is known for its scenic beauty, outdoor recreational opportunities, and close-knit community. The city offers various amenities including parks, hiking trails, and a vibrant downtown area with local businesses and shops. Waukon is also home to a number of annual events and festivals that attract visitors from all over the region.