The purpose of this study was to monitor the presence of Cryptosporidium spp. and Giardia duodenalis in a water treatment plant (WTP) using settling sludge and backwash water (BW) samples in previous and post the deflocculation of polyaluminium chloride (PAC) flacks. Eleven collections were performed. BW and settling sludge (SSF) were concentrated by calcium carbonate flocculation, and another aliquot of settling sludge (SSC) by centrifugation. The samples were divided as follows: Group A, containing 33 samples without degradation of PAC flakes, and Group B, with degradation by alkalinization with 10 M NaOH. Sample DNA was extracted with a commercial kit, and nested polymerase chain reaction (PCR) was used to detect Cryptosporidium and G. duodenalis. All samples from Group A were negative for Cryptosporidium spp., and 6.1% (2/33) were positive for G. duodenalis in SSC samples. While the absence of Cryptosporidium may be due to a low contamination level of the water resource, the presence of G. duodenalis indicates contamination of the raw water. The detection of G. duodenalis in SSC samples indicates that this detection method was the most effective. The 33 samples from Group B were negative for both protozoa, probably due to the presence of aluminium and humic substances.