Free-living amoebae can potentially cause infections in humans and animals. Contaminants in the water can affect water quality and, consequently, human health. A total of 68 tap water samples were collected during a one-year period to evaluate the quality of tap water in six districts in Fayoum Governorate according to free-living amoebae, bacteriological and physicochemical aspects. All parameters of water were tested according to the standard methods for the examination of water and wastewater. Overall, the detection rate of free-living amoebae in tap water samples was 39.7% (27/68). Seasonally, the highest detection rates of free-living amoebae were recorded during the autumn months (52.9%), followed by spring (47.1%), summer (35.3%) and winter (23.5%). We found no correlation between free-living amoebae and water quality parameters except for temperature. In conclusion, surveillance of FLAs in water resources is an important task for controlling the transmission of these pathogens.