Water is the most important source of life for humans and wildlife. Drinking water pollution is a major problem in Lithuania and the rest of the world. Private water wells and wells used for central supply in rural areas are particularly sensitive to pollution. Lithuania has sufficient water resources, but it is very important to ensure good quality of water. As a result of pollution water quality is deteriorating. This restricts the use of water and poses a threat to our health and the functioning of aquatic ecosystems. Furthermore, this reduces the number of available water sources for consumption. Earlier studies conducted in Lithuania evaluated the microbiological quality of drinking water only on the basis of the legislation on quality requirements for drinking water (HN 24: 2003) i.e. it was evaluated according to the three microbiological indicators: coliform bacteria, Escherichia coli, and faecal enterococci (Enterococcus faecium) count (microbiologically clean water should not contain any microorganisms). In addition to these three indicators of faecal water contamination, the present research for the first time in Lithuania identifies other microorganisms, such as Pseudomonas spp., Aeromonas spp, Acinetobacter spp., and bacteria of CDC group No-1 using molecular methods.