A microbiological water analysis is mainly based on the concept of fecal indicator bacteria. This study was conducted to evaluate some private groundwater wells and groundwater well based-plants in the Assuit Governorate during the summer and autumn of 2013. With the assessment of the presence of thermotolerant fecal coliform and thermotolerant fecal streptococci bacteria as potent indicators for fecal contamination, we used multiple-tube fermentation or membrane filters for enumerating the thermotolerant fecal coliform and thermotolerant fecal streptococci using the most-probable-number (MPN) index. In this study, we used 178 water samples. The results showed that there were 9 water wells not suitable to be consumed as drinking water for humans with an additional 5 other wells suddenly contaminated in the autumn so as to need a continuous sterilization system; 2 water well plants and 2 water networks needed replacement and renovation. In addition, 4 other water well plants and 4 water networks suddenly contaminated in the autumn had to be treated and disinfected before usage for drinking or human consumption. The physicochemical parameters of the water samples of the most studied locations were in permissible limits of the Egyptian standards for drinking water.