This report attempts to give a survey from literature on the microorganisms involved, on the factors and mechanisms potentially relevant for the susceptibility of drinking water wells to health related microbial contamination. The habitat groundwater accommodates a rich diversity of microorganisms, which has only begun to be identified since the development of molecular detection methods in addition to the conservative cultivation techniques. Characteristics of the subsurface are darkness, low spaces, low nutrient and low oxygen content. Indigenous microorganisms have adapted to these oligotrophic conditions and are able to proliferate in this environment permanently. Other incoming microorganisms generally cannot reproduce under these conditions, but have developed strategies to survive. They can grow only, when the parameters turn favourable. Pathogenic microorganisms comprise bacteria, viruses, and protozoa, which can also survive a certain time in groundwater. Most microorganisms in the subsurface are attached to surfaces and survive best within biofilm populations. Pathogenic microorganisms originate from human or animal faeces. These organisms are not easily detected. The methods are very time and labour consuming. Therefore, other microorganisms regularly present in the faeces are used for detection. Their presence indicates the possibility of a contamination with pathogens. As indicator microorganisms mostly coliform bacteria, E. coli, enterococci and clostridia are used. Contamination with pathogens is reported to derive essentially from communal sources: defects in wastewater treatment plants, sewage tanks, pipes, and waste deposits; from agricultural sources: animal wastes, liquid manure, and grazing; and from point sources like faeces from animals, birds, and humans. Entrance into the subsurface occurs via rainwater and surface waters, as well as by direct contamination of wells. The transport of the microorganisms into the subsurface is influenced by the geologic conditions of a specific site: soil and rock type, presence of fissures, heterogeneity. In sand, microbial movement is less far than e.g. in Karst regions, thus the susceptibility to contamination of groundwater and wells is lower. Pore sizes are crucial for sedimentation and filter efficiency of the soil. Also important is the extent of the unsaturated zone, the flow velocity of the groundwater, the geochemistry and mineralogy of the site. Wells receive their water from the groundwater reservoir of the surrounding soil. The quality of the well water is therefore essentially dependent on the properties of the groundwater and all the factors influencing the groundwater may also be relevant for the well water. The wells represent, in addition, a separate complex system with specific conditions and influencing parameters. This specific habitat involves additional variable adsorption surfaces, more space, higher flow velocity of the water, a mixing of waters from different groundwater layers and thus a different chemical composition. Contamination may also arise from microbial introduction at the open wellhead. Two main processes have been identified which are essentially responsible for the elimination of pathogens during their pathway from top of the soil to the extraction well: inactivation of the microorganisms and their adsorption to the soil particles in the subsurface. Both processes are influenced by a variety of factors and conditions present at a given site. To mention are here properties of (i) The soil: consistence and texture of surfaces, electric charge, hydrophobicity, degree of moisture, coating with organic material. (ii) The groundwater: temperature, pH, presence of cations and ionic strength, presence of organic substances, dissolved oxygen content, activity of indigenous microorganisms. (iii) The microorganisms: forming of flagella, fimbria, hydrophobicity of the cell surface, forming of extracellular polymeric substances, forming of cysts and spores as survival strategies. In addition to the description of the microbial diversity in the subsurface, the sources of pollution and the factors controlling the microbial pathways into groundwater and wells, main methods for the detection of a variety of contaminating microorganisms are given at the end of the report.