The quality of drinking water and its health implications for school children were examined at schools in the Santarém region, Amazon, Brazil. In this region, the population is fully supplied by groundwater from the voluminous Alter do Chão aquifer. Drinking water samples from three schools in Santarem city and from one school at the rural Mojuí dos Campos town were subjected to microbiological and physicochemical compositional analyses. The health risk of human exposure to chemical compounds through water intake was also evaluated. The results indicated that most water samples were contaminated with total coliform and with E. coli, which could cause serious intestinal disorders for school children. Drinking water was acidic and most of the chemical element concentrations were within Brazilian water potability recommended levels. One exception was the high aluminium content in schools from Santarem served by shallower wells, suggesting that further epidemiological studies are necessary and the monitoring of exposed school children should not be discarded. Elevated nitrate concentrations were also noted in schools from Santarém with shallower wells, indicating lack of sanitation and the importance of periodic monitoring of drinking water to prevent adverse health effects. Quantification of human health risk indicated a hazard in schools served by shallower wells, with aluminium as the main pollutant, followed by nitrate. The results showed that most drinking water quality parameters are in accordance with Brazilian legislation. However, microbiological contamination, water acidity, aluminium and nitrate concentrations must be taken into consideration for local governments in order to prevent related diseases among school children.