Hurricanes often flood homes and industries, spreading pathogens. Contact with pathogen-contaminated water can result in diarrhea, vomiting, and/or nausea, known collectively as acute gastrointestinal illness (AGI). Hurricanes Matthew and Florence caused record-breaking flooding in North Carolina (NC) in October 2016 and September 2018, respectively. To examine the relationship between hurricane flooding and AGI in NC, we first calculated the percent of each ZIP code flooded after Hurricanes Matthew and Florence. Rates of all-cause AGI emergency department (ED) visits were calculated from NC's ED surveillance system data. Using controlled interrupted time series, we compared AGI ED visit rates during the three weeks after each hurricane in ZIP codes with a third or more of their area flooded to the predicted rates had these hurricanes not occurred, based on AGI 2016-2019 ED trends, and controlling for AGI ED visit rates in unflooded areas. We examined alternative case definitions (bacterial AGI) and effect measure modification by race and age. We observed an 11% increase (rate ratio (RR): 1.11, 95% CI: 1.00, 1.23) in AGI ED visit rates after Hurricanes Matthew and Florence. This effect was particularly strong among American Indian patients and patients aged 65 years and older after Florence and elevated among Black patients for both hurricanes. Florence's effect was more consistent than Matthew's effect, possibly because little rain preceded Florence and heavy rain preceded Matthew. When restricted to bacterial AGI, we found an 85% (RR: 1.85, 95% CI: 1.37, 2.34) increase in AGI ED visit rate after Florence, but no increase after Matthew. Hurricane flooding is associated with an increase in AGI ED visit rate, although the strength of effect may depend on total storm rainfall or antecedent rainfall. American Indians and Black people-historically pushed to less desirable, flood-prone land-may be at higher risk for AGI after storms.