Antibiotics have been widely detected in the water environment and thus pose a potential threat to human health. Although antibiotics have health-promoting properties, whether and how they affect health at environmental concentrations remains uncharacterised. We detected antibiotics in surface water and groundwater in China. Sulfonamides (851 ng/L) and tetracyclines (1322 ng/L) showed the highest concentrations in surface water, while the highest concentration of sulfonamides detected in groundwater was 250 ng/L. We analysed the distribution of four classes of antibiotics (sulfonamides, tetracyclines, macrolides, and quinolones) and evaluated the associated health risks in the surface water of seven cities. We found that antibiotic pollution caused health risks to the 0–3-months age group, but not to other age groups. We further demonstrated that simulated long-term exposure to environmental concentrations of antibiotics had concentration-dependent toxic effects on L-02 hepatocytes, affected cell proliferation, and induced oxidative damage and DNA damage. Chronic exposure to mixed sulfonamides affected growth, caused liver damage, and reduced the abundance of intestinal flora in mice. Under exposure to antibiotics, the abundance of Helicobacter pylori in the gut flora significantly increased and posed a health risk to humans. These results indicated that exposure to antibiotics at environmental concentrations can cause oxidative damage and inflammation both in vitro and in vivo. These findings add to the body of basic data on the distribution of antibiotics in the water environment, and provide a scientific basis for the evaluation of antibiotic toxicity.