The presence of waterborne pathogens, when associated with the water supply system, poses risks to public health. This study investigated the occurrence of (oo)cysts of Cryptosporidium spp. and Giardia spp. in two Water Treatment Plants, with full-cycle technology, and assessed the microbiological risk to consumers’ health. The membrane filtration technique was employed to identify the protozoan load in 24 samples of raw and filtered water. Physicochemical and bacteriological parameters were also analyzed. The Quantitative Microbial Risk Assessment model was used to determine the risk of daily and annual infection associated with the ingestion of filtered water. A total of 66.67% of raw water samples were positive for Cryptosporidium; and 33.33%, for Giardia. The maximum concentrations of 200 (oo)cysts/L and 50 cysts/L were detected in the Cerrado stream (located in Sanclerlândia, state of Goiás, Brazil), due to the predominance of grazing areas and intense agricultural activity. Water Treatment Plants did not completely remove the protozoa and the retention efficiency was lower than that recommended by the United States Environmental Protection Agency, with average values of 1.27 log for cysts and 1.04 log for oocysts. The probability of annual infection by cysts (100%) was higher than that of oocysts (86.61 - 98.32%) as for consumption of filtered water, and in the dry season, there was a higher risk of infection, due to the low performance of the Water Treatment Plants and higher concentration of pathogens. According to the results, the continuous intake of filtered water above the warning level can cause infectious diseases in the supplied population.
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