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The biofilms and water samples from a model installation built of PVC-U, PE-HD and cast iron pipes were investigated using standard heterotrophic plate count and 16S rRNA Next Generation Sequencing. The results of the high throughput identification imply that the construction material strongly influences the microbiome composition. PVC-U and PE-HD pipes were dominated with Proteobacteria (54-60%) while the cast pipe was overgrown by Nitrospirae (64%). It was deduced that the plastic pipes create a more convenient environment for the potentially pathogenic taxa than the cast iron. The 7-year old biofilms were described as complex habitats with sharp oxidation-reduction gradients, where co-existence of methanogenic and methanotrophic microbiota takes place. Furthermore, it was found that the drinking water distribution systems (DWDS) are a useful tool for studying the ecology of rare bacterial phyla. New ecophysiological aspects were described for Aquihabitans, Thermogutta and Vampirovibrio. The discrepancy between identity of HPC-derived bacteria and NGS-revealed composition of biofilm and water microbiomes point to the need of introducing new diagnostical protocols to enable proper assessment of the drinking water safety, especially in DWDSs operating without disinfection.