Since 2005, over 30 epidemiological studies have evaluated the association between nitrate in drinking water and adverse health outcomes. Conditions that lead to nitrate pollution in water, such as open defecation, the proximity of septic tanks to water sources, and the use of inorganic fertilizer, are rampant in Indonesia, which has experienced little research evaluating nitrate in drinking water. We conducted a health risk assessment for exposure to nitrate in drinking water and evaluated the nitrate concentration in key water sources in two villages of rural Central Java, Indonesia. The nitrate concentrations in the drinking water ranged from 3.55 mg/L to 26.75 mg/L as NO3−. Daily nitrate intake estimates, calculated at 50% and 95% exposure to the maximum nitrate concentration of the drinking water in both villages, were above the levels associated with birth defects, colorectal cancer, and thyroid conditions observed in other studies. There was a large variation in nitrate concentrations between and within the villages at different water sources. Further research into whether these health outcomes exist in rural Central Java, Indonesia will be required to better understand this risk.