Studies investigating the correlation between metal content in water and metal levels in children are scarce worldwide, but especially in developing nations. Therefore, this study investigates the correlation between arsenic, chromium, and mercury concentrations in drinking and cooking water and in blood and urine samples collected from healthy and supposedly non-exposed children from a rural area in Yucatan, Mexico. Mercury in water shows concentrations above the recommended World Health Organization (WHO) value for drinking and cooking water. Also, 25% of the children show mercury in urine above the WHO recommended value. Multivariate analyses show a significant role for drinking and cooking water as a vector of exposure in children. Also, the factor analysis shows chronic exposure in the case of arsenic, as well as an ongoing detoxification process through urine in the case of mercury. Further studies should be done in order to determine other potential metal exposure pathways among children.