From the Wardian wastewater treatment plant in Alexandria, 48 water samples were collected and filtered through nitrocellulose membranes and placed on non-nutrient agar with Escherichia coli to cultivate free-living amoebae (FLAs). Results revealed that the occurrence of FLAs reached 75.0% and 62.5% in raw and treated wastewater samples, respectively. Morphological identification of FLAs from raw and treated wastewater samples showed that 45.8% and 37.5%, respectively (from the positive samples) belong to the genus Acanthamoeba. Whereas, other FLAs belong to the other genera in raw and treated water samples that reached 29.2% and 25.0, respectively. The treated water process of the plant removed only 12.5 % of FLAs. Statistically, seasons recorded no significant effect on the prevalence of FLAs in the wastewater samples. 85.0 % from the morphologically identified Acanthamoeba spp. were confirmed, when molecularly tested using a simple PCR technique. In conclusion, the presence of FLAs in treated wastewater leads to direct and indirect public health hazards as they may harbor other pathogenic microorganisms that can escape from the wastewater treatment processes and reach the end-user.