The magnitude and spatial variability of acute gastrointestinal illness (AGI) cases attributable to microbial contamination of U.S. community drinking water systems are not well characterized. We compared three approaches (drinking water attributable risk, quantitative microbial risk assessment, and population intervention model) to estimate the annual number of emergency department visits for AGI attributable to microorganisms in North Carolina community water systems. All three methods used 2007-2013 water monitoring and emergency department data obtained from state agencies. The drinking water attributable risk method, which was the basis for previous U.S. Environmental Protection Agency national risk assessments, estimated that 7.9% of annual emergency department visits for AGI are attributable to microbial contamination of community water systems. However, the other methods' estimates were more than 2 orders of magnitude lower, each attributing 0.047% of annual emergency department visits for AGI to community water system contamination. The differences in results between the drinking water attributable risk method, which has been the main basis for previous national risk estimates, and the other two approaches highlight the need to improve methods for estimating endemic waterborne disease risks, in order to prioritize investments to improve community drinking water systems.