The delivery of safe drinking water services depends on effective role played by stakeholders. From the parasitological point of view, the Egyptian standards for drinking water denied the presence of any type of living protozoan parasites in potable water produced for human use. In the present study, raw and treated water samples were separately collected from a conventional drinking water treatment plant (DWTP) and a compact unit. They were concentrated through nitrocellulose membrane filters (0.45µm pore size). The concentrate of each sample was examined with both light microscopy and PCR. Six genera of parasitic Protozoa (Giardia, Cryptosporidium, Entamoeba, Balantidium, Cyclospora and Isospora) and a group of microsporidial spores were detected in inlet water samples of the two examined treatment systems. Microscopically, the obtained data declared that 70.8% and 83.3% of inlet water from conventional DWTP and compact unit, respectively were contaminated with parasitic protozoa. The encountered parasitic protozoa in inlets of examined DWTPs were only microsporidial spores representing 8.3% and 16.7% of treated water from conventional DWTP and compact unit, respectively. Removal of protozoan parasites was higher in conventional DWTP (82.4%) than in compact unit (75%). Molecularly, the presence of protozoan parasites in the outlet of the compact unit was higher than in the outlet of the conventional DWTP. In general, molecular detection of protozoan parasites revealed a little bit lower or equal (in some instances) prevalence than that obtained by microscopy. In conclusion, most of inlet water samples from both conventional DWTP and compact unit were contaminated with protozoan parasites. Although conventional DWTP was more effective than compact unit for removing parasitic protozoa, l some of these parasites could be still detected in treated water and thus reach to consumers and cause health hazards.