Walkerton was originally part of Brant Township and was first settled in 1849 by William Jasper and Edward Boulton who farmed to the east of the river.

Other settlers from the same era included John Lundy, Moses Stewart and Thomas Bilkie who farmed to the west of the river.

The water supply was contaminated as a result of improper water treatment following heavy rainfall in late April and early May 2000, that had drawn bacteria from the manure of nearby cattle used to fertilize crops into the shallow aquifer of a nearby well.

The contamination caused gastroenteritis and sickened more than 2,000 people and resulted in seven deaths, and left others with chronic illnesses.

The town was rumoured to have been placed in the Guinness World Records for having a church on each corner of the jail and courthouse complex.