The description of a microbiological community of drinking water distribution systems is intended for a safe and proper use of drinking water. These studies were aimed at characterising the microbial condition of the drinking water supply system in Lithuania by means of culture-based methods and biochemical techniques. Samples of drinking water (in cities supplied in centralised way from taps, wells, and boreholes) were collected in different locations in Lithuania. Seeking to grow microflora present in water the membrane filtration method was applied to study the samples. Most often water samples were studied to identify coliform bacteria (Citrobacter spp., Enterobacter spp., Klebsiella spp., Serratia spp.), Escherichia coli (or faecal coliform), Enterococci (or fecal Streptococcus), Pseudomonas aeruginosa (other non-fermentative gram-negative bacteria) according to the international ISO standards. Large amounts of non-fermenting gram-negative bacteria were found in centralised urban water. The investigation showed that more than 50% of the wells under study had increased microbial contamination with faecal coliform bacteria and faecal Streptococcus. Bacteria of the Pseudomonas group, CDC group and other non-fermentative gram-negative bacteria were detected in more than 30% samples of centralised urban water studied.