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The study of cryoconite – a specific organomineral sediment on the glacier surface – is essential to estimate environmental processes and sustainability, biogeochemical cycles, pollution rate and degree of human influence under conditions of climate change and diverse anthropogenic activities. Key chemical and physical features such as pH values, total organic carbon and hot-water extractable carbon content, microbial respiration, and particle-size distribution, as well as the content of some trace elements and pollution indices have been determined in materials sampled at the Mt. Elbrus region. The results obtained showed accumulation of easily decomposable carbon and correlated with it high rate of microbial respiration at the Garabashi Glacier, despite the low content of total organic carbon (max. 0.92%) due to its redistribution. Cryoconites at the Garabashi Glacier also efficiently accumulated trace elements, especially Zn (max. 55.40 mg kg− 1) and Pb (max. 26.03 mg kg− 1), up to high pollution level. Domination of silt and sand fractions indicated major role of autochthonous transfer to the glacial zone both from anthropogenic and natural geologic sources. Translocation of cryoconite material to the periglacial zone and anthropogenic activities led to accumulation of both total organic carbon and hot-water extractable carbon as well as trace elements such as Zn (max. 64.40 mg kg− 1) and Cd (max. 0.41 mg kg− 1) in studied Leptosols. Migration of elements from the glacial to the periglacial zone at the Elbrus region can accelerate developments of soils after glacier retreat, while intensification of human activity may pose additional pollution risks for agriculture, tourism and environmental sustainability.