Soils in urban areas are exposed to input of pollutants from many sources. Aside from the anthropogenic sources of pollution, lithology additionally greatly impacts the concentration of specific elements in soils due to soil formation from the parent substrate. Other factors need to be taken into consideration as well, such as granulometry, pH, total content of carbonates and organic matter. On the administrative area of the city of Zagreb, soil profiles were opened and morphologically tested at locations differing in lithology as well as the means of use and landscape maintenance. Soil samples were collected from genetic soil horizons to determine basic chemical and geochemical properties, including concentrations of potentially toxic elements as defined in the directive Ordinance on the Protection of Agricultural Land from Pollution: cadmium, chromium, copper, mercury, nickel, lead and zinc. The variations of concentrations in potentially toxic elements are statistically analysed with profile depth, to differentiate geological from anthropogenic effects on the contents of elements in the soils. It has been determined that soils in Zagreb are generally not contaminated, and enrichments can be interpreted as either geogenic in origin, in the case of widely distributed enrichments of lower concentration levels, or anthropogenic in origin in the case of localized high enrichments of element concentrations.