Bottom sediment pollution with heavy metals of the Sventoji River in Ukmerge, Lithuania using X-ray fluorescence spectrometry is analyzed in this article. During the research, qualitative and quantitative parameters of heavy metal concentrations and their distribution were investigated. This article presents obtained results of study, where bottom sediment samples were examined from both shores of the river of Sventoji. During this research, received data was treated using GIS software, which helped to interpolate the data of concentrations into the research polygon of the river. GIS software also helped to evaluate the urban runoff influence to the bottom sediment quality and exclude sources of pollution. The runoff dischargers which transport surface wastewater to the river were registered before sampling. At the mouth of streams, flowing into the river of Sventoji, additional samples were taken. After comprehensive river bottom sediment research there is a possibility to assess the extent of anthropogenic activity and its impact on the river ecosystem and human health.