There have been a number of outbreaks associated with drinking water, but the risk of contamination to a food establishment is dependent upon the types of processes run. So it is important to conduct a risk analysis, considering you water source, the types of contaminates that can be present, and the impact of your processes on those contaminates.
The types of contaminates in water can be found on the EPA website (US Environmental Protection Agency. Drinking water contaminants. http://www.epa.gov/safewater/contaminants/index.html).
General information on well water can be found on the CDC Websites: