Water quality monitoring of national rivers has always been a difficult task. The major problem today is to improve the water quality from the natural aquatic environments, as the demand from different sectors and to improve the capacity of water supply for domestic, agriculture, industry, energy and other uses. Microbiological contamination of water is an important worldwide problem. Aquatic ecosystems are currently threatened by demographic increase, accompanied by the increase of agricultural and industrial activities. Therefore, detection of biological sources of water contamination is essential for proper watershed management to maintain quality goals according to legal previsions. The aim of the study was to investigate the microbiological contamination status for water quality from different areas of Lower Danube Euroregion, Galati and Tulcea regions. The microbiological indicators analysed was total aerobic mesophilic bacteria, as indicator of organic pollution and coliform bacteria, as indicator microorganisms for prediction of faecal contamination and possible pathogens presence. It was observed that the microbiological quality of the investigated groundwater and surface water streams region indicate a low level of contamination with faecals. The type and level of contamination should be variable in the time based on sources of contamination, season, place and sampling design. In order to improve water quality, it is important to set up a management strategy and plans that provide implementing strategies to address water quality.