The aim of this study was to assess the carcinogenic and non-carcinogenic health risks of nine heavy metals including arsenic, cadmium, chromium, copper, iron, nickel, lead, selenium and zinc in the Isfahan-Barkhar and Kashan aquifers. 33 samples (18 samples from Isfahan-Barkhar aquifer and 18 samples from Kashan aquifer) were collected in 1403 and the concentrations of heavy metals were measured using an ICP-MS device. The health risk assessment was carried out based on the guidelines of the United States Environmental Protection Agency (USEPA) and by calculating the Chronic Daily Intake Index (CDI), Hazard Quotient (HQ), Hazard Index (HI) and Incremental Lifetime Carcinogenic Risk (ILCR) for children and adults. The results showed that arsenic was the most important factor causing health risks in both aquifers, while nickel and zinc also increased the risk indices in some places. In a number of samples, their concentrations exceeded the permissible limits of the World Health Organization (WHO). The arsenic HQ index in both aquifers exceeded the acceptable limit (HQ>1) for both age groups. Also, 44.4 and 66.7 percent of the samples from the Isfahan-Barkhar and Kashan aquifers for adults, and 77.8 and 100 percent of the samples for children, respectively, had a cumulative hazard index (HI>1). ILCR values were also estimated to be higher in the Kashan aquifer for both age groups than in the Isfahan-Barkhar aquifer. Overall, the results showed that the Kashan aquifer is in a more unfavorable state in terms of health risk and children are the most vulnerable group to exposure to heavy metals.