The microbiological contamination of groundwater has profound and severe implications for public health, particularly in small communities and developing countries where groundwater is often the preferred source of drinking water. Although natural groundwater is usually of good quality, this can deteriorate rapidly due to inadequate source protection and poor resource management. Contaminated groundwater can contribute to high morbidity and mortality rates from diarrhoeal diseases and sometimes lead to epidemics. The disposal of excreta using land-based systems is a key issue for groundwater quality and public health protection. The use of inappropriate water supply and sanitation technologies in peri-urban areas leads to severe and long-term public health risks. The use of poorly constructed sewage treatment works and land application of sewage can lead to groundwater contamination close to water supply sources. Microbiological, in particular virus survival in these circumstances is not well understood, but there are indications of extended pathogen survival and therefore increased public health risk.