Groundwater is the only source for drinking water supply in Lithuania. Twenty water intakes exploiting Quaternary aquifers are operating in Vilnius City. The main aim of this study was to characterize the heavy metal content of internal pipeline sediments in the water supply network. It also provides a new insight into the accumulation of phosphorus and its variation in pipeline sediments in the study area. The results of this research reflect the level of heavy metals that accumulated during the water supply process. The main microelements detected were lead, nickel, zinc and copper. The research results will be useful for conducting preliminary evaluations of possible microelement accumulation in other similar water supply systems. The evaluation of water supply sediments is considered as one of the most important activities associated with a water safety approach. The results of this research indicate the dependence between phosphorus accumulation and Pb, Cr, Zn, Ni and Cu quantities in the internal sediments of water supply pipelines.