Enteric pathogenic protozoa like Giardia and Cryptosporidium pose significant health risks, especially in Egypt; they contaminate drinking water. Giardia is known for causing giardiasis, while Cryptosporidium leads to cryptosporidiosis, both of which can result in severe gastrointestinal symptoms. The presence of these protozoa in water sources is often linked to inadequate sanitation and water treatment practices, making it essential to address issues related to water quality. Control of waterborne diseases is critical for public health, and drinking water treatment plants (DWTPs) play a central role in this effort through employing various treatment processes such as coagulation, filtration, and disinfection. DWTPs effectively remove contaminants and pathogens from water sources. It is true that not much study has been done on the use of immunofluorescence assays (IFA) to monitor Cryptosporidium and Giardia species in developing countries including Egypt. These techniques can significantly enhance the detection and quantification of these parasites compared to traditional methods. Water samples (10 liters volume each) were collected monthly at the same time from each sampling site for a year from January 2023 to December 2023, from both the inlet (raw freshwater) and outlet (final treated drinking water) of two conventional DWTPs (Shebin and Tala). The samples were collected from the inlet and outlet of each DWTP and were processed by immunofluorescence assay. The examination of 48 collected water samples from inlet and outlet of Tala and Shebin DWTPs revealed the occurrence of Giardia cyst and Cryptosporidium oocyst in 58.3 % (14/24) and 54.2 % (13/24) of collected raw water respectively, on other hand the occurrence of Giardia, Cryptosporidium and in outlet samples were 16.7 % (4/24) and 12.5 % (3/24), respectively.