In 1996, two friends, Mike McElwain and Jerome Ebel, bought an old brick building on Highway 10 in Junction City, Wisconsin. The building, built around 1920, was originally a Model-A Ford dealership. Subsequently, the building housed a barbershop, followed by a liquidator of second-hand goods, before being vacated in 1988. Mike and Jerome purchased the building in 1996, and spent the next two years thoroughly cleaning and restoring it. When the facility was ready for its first beer production, the friends put together the funds to purchase some used dairy equipment. This equipment was retrofitted to ultimately become the brewery's first brew house. Months later, Central Waters Brewery came to be.

Mike and Jerome began production using their own home brewing recipes. The initial brews were offered in growlers, 12 and 24 ounce bottles, and kegs. The original lineup included: Ouisconsing Red Ale, Happy Heron Pale Ale, and Mudpuppy Porter. The pair also made an award winning barley wine; in 2000, Kosmyk Charlie's Y2K Catastrophe Ale captured a bronze medal at that year's World Beer Cup.

Within a few months of the first beer production, Paul Graham was hired to help Jerome and Mike so that they could maintain their full-time jobs. The partners' start up was part of a national trend toward producing bigger and better beers at the small, local level. The exact opposite of what most Americans had seen since the emergence of modern refrigeration and big, national brands, these microbreweries revisited pre-prohibition recipes, and further developed them to include most varieties brewed around the world.

After three years under the original ownership, the brewery went up for sale. Brewer Paul Graham teamed up with avid home-brewer and literal "beer fanatic," Clint Schultz, to purchase the building, equipment, and recipes. This move secured the place of craft brewing in Central Wisconsin. While the original beer list was good, Clint and Paul had ideas of their own. They expanded on the original lineup by turning seasonal favorites, Lac Du Bay India Pale Ale (IPA) and Satin Solstice Imperial Stout, into regular brews. In addition, they also wanted to offer bottles in six packs. In order to achieve this, the duo acquired an automated bottling machine.

Shortly after the acquisition of the bottling machine, the original brew house fired for the last time. Not being designed for the stress it was enduring, the main brew kettle cracked beyond repair. On its five-year anniversary, Central Waters purchased a 15-barrel brew house, and two 30-barrel fermenters to support the larger batches produced by the new brew house.

In early 2006, Clint Schultz left the brewery to pursue other interests. The brewery is now owned and operated by Paul Graham and Anello Mollica, who bring over 24 years of brewing experience into the company.

Currently, Central Waters Brewing Company services over 200 retail locations in Central Wisconsin, and has expanded its product line to include 18 beer styles. Moving from Junction City to a new facility in Amherst, Wisconsin in January of 2007, Central Waters can better support the growing demand. CWBC continues to build on the solid reputation of producing the finest quality beers in Central Wisconsin.