Surface runoff from urbanized territories carries a wide range of pollutants. Sediments in untreated runoff from direct discharge stormwater systems significantly contribute to urban waterway pollution. In this study, heavy metal (Pb, Zn, Cu, Cr, Ba, As and Fe) contamination in surface runoff sediments of the urban area of the city of Vilnius was investigated. The surface runoff sediment samples were collected from seven dischargers with the highest volume rate of water flow and concentrations of suspended solids. The geospatial analysis of the distribution of heavy metals shows that there are several active pollution sources supplying the dischargers with contaminated sediments. Most of these areas are located in the central part of the city and in old town with intense traffic. Principal components analysis and t-test results clearly depicted the significantly different chemical compositions of winter and autumn surface sediment samples. The sampling approach and assessment of results provide a useful tool to examine the contamination that is generated in urban areas, distinguish pollution sources and give a better understanding of the importance of permeable surfaces and green areas.