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