This article presents the results of long-term research and monitoring of the soil cover exposed to the impact of the mining and processing plant developing diamond deposits in the northeast of Siberia. The soil collection includes 436 samples of different types of Cryosols. Soil pH; soil organic carbon (SOC); granulometric composition; and mobile forms of Pb, Ni, Mn, Cd, Co, Cr, Zn, Cu, and As were identified in the samples. Multivariate statistics of the correlation matrix, clustering analysis (CA), and principal component analysis (PCA) were used to determine the sources of heavy metals. The intensity of the accumulation of chemical elements in the soil was assessed using calculated concentration coefficients (Kc) and the index of total contamination of the soil cover (Zc). In the study area, Cryosols are characterized by biogenic accumulation of Ni, Mn, and Cd in the upper soil layer and Cr, Ni, Co, Mn, and Cu in the suprapermafrost horizon. Correlation matrix, CA, and PCA revealed three distinct sources that could be considered for the investigated potentially toxic elements (PTEs): anthropogenic, lithogenic, and the source which comes from a mixed contribution of anthropogenic and lithogenic factors. The most anthropogenic contribution in the heavy metals in the study area appears in Zn, Cd, As, and Pb. The assessment interpreted that origin of Mn in the area is most likely to be a natural source. The content of Co, Cr, and Ni are controlled by both lithogenic control and anthropogenic sources. Active accumulation of mobile forms of Mn, Zn, and Ni with anomalously high concentration coefficients can be traced in the soils in the impact zone of mining operations. Anthropogenic soil contamination is spread over an area of 260 km2.