The climate warming–related degradation of permafrost can lead to the entry of climatically and biologically active substances, including mercury, into the biosphere; this work focuses on the analysis of the total content of mercury and organic carbon in 15 cores drilled in frozen Quaternary deposits of the Arctic Archipelago of Spitsbergen. The mercury content was additionally analyzed in bedrock samples, because the studied Quaternary deposits are formed by the weathering of the bedrock of the area. The results show that mercury concentrations in 157 studied samples of frozen Quaternary deposits range from 21 to 94 ng/g, with an average value of 40 ng/g. The expected correlation of mercury content with organic carbon content is not revealed. There are no trends in the accumulation of mercury depending on the lithological facies, geomorphological position, the time of sedimentation, or the freezing conditions. The average content of mercury in bedrock is relatively low, with a mean value of 8 ng/g. This means that the main source of mercury in frozen Quaternary deposits is not bedrock, but the formation of organic matter complexes or sorption on clay particles. In terms of the ongoing discussion about mercury input from permafrost to ecosystems, the results obtained from boreholes can be considered preindustrial background values.