The first white settlers in the area were Yankees, Germans and Luxembourgers who arrived in the 1840s, but the community was rural until the 1870s when the Chicago, Milwaukee & St. Paul Railway built a station in the area and businesses began to cluster it, laying the foundation for the village.

Today, Waubeka is home to the National Flag Day Foundation headquarters and its Americanism Center Museum, which has an extensive collection of patriotic memorabilia.

While many Native people moved west of the Mississippi River to Kansas, some chose to remain and were referred to as "strolling Potawatomi" in contemporary documents because many of them were migrants who subsisted by squatting on their ancestral lands, which were now owned by white settlers.

One such group was led by Chief Waubeka, who maintained a winter camp in the Ozaukee County community that bears his name as late as 1845.

The area has some subterranean Silurian limestone formations that are part of the Racine Dolomite that stretches through eastern Wisconsin and Illinois.

There were also white cedars growing along the Milwaukee River, which flows along the village's western boundary.

[14] As land development continues to reduce wild areas, wildlife is forced into closer proximity with human communities like Fredonia.

Large mammals, including white-tailed deer, coyotes, North American river otters and red foxes can be seen in the village.

Many birds, including great blue herons and wild turkeys are found in the village.

[15] The region struggles with many invasive species, including the emerald ash borer, common carp, reed canary grass, the common reed, purple loosestrife, garlic mustard, Eurasian buckthorns, and honeysuckles.

Fredonia is home to the Divine Savior Catholic Congregation, which operates the St. Rose of Lima Chapel and a parochial school for kindergarten through eighth grade in the village.

The congregation also offers services at Holy Cross Chapel in Holy Cross and Our Lady of the Lakes in Random Lake,[18] and also maintains the historic building and cemetery of St. Mary Mother of Sorrows Church in the hamlet of Little Kohler.

[19] St. John Lutheran Church, affiliated with the Missouri Synod, is also located in the Village of Fredonia.

The current Administrator is Christophe E. Jenkins - who was formerly the Mayor of the City of West Bend, WI.

[23] [24] As part of Wisconsin's 6th congressional district, Fredonia is represented by Glenn Grothman (R) in the United States House of Representatives, and by Ron Johnson (R) and Tammy Baldwin (D) in the United States Senate.

Located at the Riveredge Nature Center in the northwestern Town of Saukville near the municipal boundary with the Village of Newburg, the school serves children from kindergarten through fifth grade.

[30] Divine Savior Congregation operates a Catholic parochial school in the village offering kindergarten- through eighth grade education.

The Village of Fredonia maintains seven public parks with amenities including playgrounds, baseball diamonds, soccer fields, picnic shelters, and ice-skating rink, and an eighteen-hole disc golf course.