This study presents an assessment of the protection provided by water intake and treatment systems against potential health risk to water consumers. To perform the assessment a case study was conducted involving modelling and risk assessment based on scenarios of decreasing water quality at the intakes (i.e. emergency situations). The study sites were two continuously operating water treatment plants in Southern Poland (CEE). The study material were the results of tests conducted in the years 2012–2019 on samples of water taken directly at the intakes and samples of treated water. The samples were used to determine the concentration of selected metals (Cd, Cr, Mn, Ni, Pb and Zn), organic pollutants (benzo(a)pyrene, benzene, acrylamide, epichlorohydrin, vinyl chloride and 1,2-dichloroethane) and bacteriological pollutants (Coliform bacteria, Escherichia coli, Enterococcus faecali and Clostridium perfringens). The non-carcinogenic (HI) and carcinogenic (CR) hazard indexes were estimated based on the quality of water at the intake using linear regression models. The risk values obtained were compared with permissible values specified in the US EPA methodology. It was demonstrated that the concentrations of the xenobiotics analysed in treated water would have to increase 11 times in the case of adults and 29 times in the case of children before the risk level related to drinking water exceeded permissible values. In the least favourable exposure scenario modelled, assuming the presence of organic xenobiotics in potable water, the total HI amounts to only 10% of the permissible value in adults and 1.5% in children. The total CR calculated for the 3-times lower water quality did not exceed permissible values, which proves that the water treatment systems are safe.