In agricultural intensive areas, drinking contaminated water from private wells is considered an important cause of acute gastroenteric illnesses (AGI), particularly among high-risk populations. In the summer of 2009, the microbial water quality of 180 randomly selected private wells in two northeastern Ohio counties, a region with a high concentration of dairy farms, was assessed. Forty-five percent (82/180) of water samples were contaminated with total coliforms. Generic Escherichia coli were present in 9% (16/180) of samples. Using real-time polymerase chain reaction, E. coli O157:H7 was identified in 4% (7/180) of specimens. Campylobacter spp. DNA could not be amplified from 70 of the samples tested for this organism. The frequency of generic E. coli contamination varied among townships (P < 0.001). Well structure (i.e. age and depth) or other common measures of pollution potential (depth of water, hydrology, topography, net recharge soil media) was not correlated with coliforms and E. coli contamination. Importantly, the presence of the pathogen E. coli O157:H7 was not associated with the presence of fecal indicators in the water samples: Only one of the seven E. coli O157-positive samples was also positive for generic E. coli. Appropriate risk management and communication processes are needed to reduce the potential waterborne disease outbreaks in agricultural intensive areas.