The management of microbial pollution sources in rural surface water is challenging. Its management programs often rely on monitoring for a large number of water quality parameters to define contaminant issues. Total coliforms, faecal coliforms, and faecal streptococci have traditionally been used to identify microbial contamination. The objective of this study was to carry out an environmental survey based on the waste drainage systems and to assess the microbial pollution of rural surface waters in thirty Egyptian villages located at Gharbia (10 villages) and Menofia governerates (20 villages). The results show that septic tanks are the most common method of sanitary drainage systems in the Gharbia Governorate villages. About 60% of the villages had both of private net work and septic tanks systems and 30% had only septic tanks systems. In Menofia Governorate the dominant system is septic tanks which covered 85% of the surveyed villages. The municipal network was found under construction in about 15% of the villages. Statistical analyses of total coliform, faecal coliform and faecal streptococci demonstrated that the maximum microbial pollution was found in Ghrbia Governorate The averages of the TC, FC, and FS concentrations were 2.11x106, 9.11x105 and 9.93x104 (MPN 100 ml-1) respectively. While in Menofia Governorate, the averages of the TC, FC, and FS concentrations were 3.25x105, 2.34x104 and 1.75x103 (MPN 100 ml-1) respectively. The stream water in all of the thirty villages sites was identified as polluted, the specific location of the contamination source has not been identified and additional microbial source tracking (MST) methods will be required.