Serious pollution of alluvial soils by a wide range of potentially toxic elements is usually observed in the valleys with mining and metallurgical industry. To outline areas of increased risk elements inputs, measurements of soil magnetic susceptibility can be used. This method is based on the measurement of the concentration of ferrimagnetic minerals of anthropogenic origin, mainly iron oxides, which are closely associated with risk elements such as heavy metals. The aim of this study is to examine the link between magnetic susceptibility of poorly drained Litavka River alluvial soils located in the mining/smelting region of Příbram (Czech Republic) and the observed high concentration of risk elements in soils. Surface volume magnetic susceptibility and the vertical distribution of magnetic susceptibility in soil profiles were measured in situ. On the basis of field measurements, selected parts of soil cores were sampled for a detailed magnetic and chemical analysis. Our results demonstrate a statistically significant correlation between magnetic susceptibility and soil concentration of Cu, Pb, and Zn. The magnetically enhanced soil layer, relatively low frequency-dependent susceptibility, presence of Verwey transition, and scanning electron microscope observations suggested a prevalence of coarse magnetite/maghemite, likely of anthropogenic origin. However, the magnetic properties in-situ also reflected the natural soil conditions and soil processes. The high content of organic matter, varying reductive/oxidative condition, and vertical migration of magnetic phases were the main factors influencing the observed magnetic susceptibility values.