Recent outbreak investigations suggest that a substantial proportion of waterborne disease outbreaks are attributable to water distribution system issues. In this analysis, we examine the relationship between modeled water residence time (WRT), a proxy for probability of microorganism intrusion into the distribution system, and emergency department visits for gastrointestinal (GI) illness for two water utilities in Metro Atlanta, USA during 1993–2004. We also examine the association between proximity to the nearest distribution system node, based on patients' residential address, and GI illness using logistic regression models. Comparing long (≥90th percentile) with intermediate WRTs (11th to 89th percentile), we observed a modestly increased risk for GI illness for Utility 1 (OR = 1.07, 95% CI: 1.02–1.13), which had substantially higher average WRT than Utility 2, for which we found no increased risk (OR = 0.98, 95% CI: 0.94–1.02). Examining finer, 12-hour increments of WRT, we found that exposures >48 h were associated with increased risk of GI illness, and exposures of >96 h had the strongest associations, although none of these associations was statistically significant. Our results suggest that utilities might consider reducing WRTs to <2–3 days or adding booster disinfection in areas with longer WRT, to minimize risk of GI illness from water consumption.