Raw water and filtered effluent of three drinking water treatment plants (WTP) at a town in Minas Gerais State, southeast Brazil, were monitored over a one-year period for Giardia, Cryptosporidium, microbiological and physical-chemical water quality indicators. High densities of Giardia and Cryptosporidium were detected in two source waters, ranging from 2.0–140 cysts/L and 4.0–510 oocysts/L. Giardia and Cryptosporidium (oo)cyst concentration was not consistently associated with most of the parameters analysed, turbidity being the most promising indicator. It also seems that Giardia and Cryptosporidium concentration was influenced by rainfall. Giardia cysts and Cryptosporidium oocysts were significantly associated in both waters, suggesting a similar pattern of occurrence and common contamination sources. In two of the three water treatment plants analyzed, Giardia and Cryptosporidium were detected in filtered effluents, also in high densities, ranging from 0.066 to 5.5 cysts/L and 0.066 to 13.2 oocysts/L, respectively. Statistical trials to associate protozoa and indicator removal failed in nearly all cases. Nevertheless, the results are interpreted as neither reaffirming nor negating the use of turbidity as a protozoa removal indicator.