This study aimed to estimate the annual probability of Giardia and Cryptosporidium infection for population supplied by contaminated drinking water sources. Parasites were quantified by USEPA 1623.1/2012 Method. Annual risk was estimated using the quantitative microbial risk assessment approach. Genotyping was performed using specific primers based on 18S rRNA gene for Cryptosporidium and gdh gene for Giardia. Giardia were detected in 83.3% of the samples (<0.1 to 8.6 cysts/L) and Cryptosporidium in 37.5% (<0.1 to 2 oocysts/L). In general, annual risks values for Giardia were 1 log above when compared to those obtained for Cryptosporidium. Giardia intestinalis A and B were present as well C. hominis and C.parvum. The lack of protection measures for water supply catchment point put population's health at risk. The results provide data to subsidize decision makers to take actions to improve environmental quality resulting in a positive impact on consumers' health.