Biodegradable compounds can cause undesired microbial growth in drinking water systems and these compounds can originate from the water or pipe materials used in drinking water systems. The aim of our study was to determine the influence of different pipe materials on the microbial populations in water and biofilm under semi-stagnant conditions. The microbial communities in biofilm and water, which were in contact with seven different materials, were characterized by determining ATP concentrations, microbial composition gene copy numbers of some specific microbial groups. The ATP concentration in water and biofilm varied between the different materials with glass (negative control) < copper < PVCC < PE-Xc < PE-Xb < PE-100 < PVC-P. Gene copy numbers of Legionella spp., Mycobacterium spp., Pseudomonas spp., Aeromonas spp., fungi and Vermamoeba vermiformis were also higher for PVC-P and PE than for glass, copper and PVCC. The bacterial community composition in water and biofilm varied between materials as well. PERMANOVA and CAP analysis demonstrated that copper and PVC-P are different when compared to the other materials. Furthermore, bacterial community composition and ATP concentrations in water and biofilm were similar after eight and 16 weeks incubation, but differed from results obtained after one week. Finally, the ATP, the specific microbial groups and the bacterial community composition also differed between water and biofilm on each material. We conclude from our study that pipe material is an important factor that influences the biomass concentration, abundance of specific microorganisms and the bacterial community composition in distribution systems with unchlorinated drinking water.