Background: Conventional drinking water treatment plants (CDWTPs) and Ground water (GWTP) are the main 2 types of drinking water treatment using freshwater as a source for drinking water in Egypt. Objective: The Egyptian standards for drinking water denied the presence of any type of living protozoa in drinking water produced for human use. Martials and methods: 48 water bodies were selected from Benha and Kaha districts in Qalyubia Governorate, Egypt. Mean turbidity, pH, conductivity, temperature, ammonia, nitrite, iron, manganese, magnesium and residual chlorine were recorded in each water body from two sites. Centrifuged samples were cultured on non-nutrient agar plates with Escherichia coli. Positive sample isolates were subjected to DNA extraction and polymerase chain reaction using genus and species-specific primers targeting the internal transcribed spacer region (ITS) and Mp2CL5 gene. Results: The prevalence of Naegleria species, N. fowleri and Acanthamoeba in the study area were 54.1% and 0% (N. fowleri and Acanthamoeba) of all sample examined. The removal of free-living amoebae from drinking water, it was shown that conventional DWTP (Benha) could get rid of 91% of FLAs present in the raw untreated water, while ground DWTP removed only 55.6% of these organisms. Conclusions: The conventional drinking water treatment system for surface water was better than that of only chlorine disinfection for ground water in removing free-living amoeba (FLAs). In general, the persistence of FLAs in drinking tap water unfortunately exerts public health hazards.