Peat organic soils play a major role in the accumulation of soil organic matter (SOM) and the mercury (Hg) cycle. Large mercury resources in peatlands can be a source of methylmercury for many decades and centuries, even if deposition is significantly reduced. The organic matter of peatland soils drained for agricultural use is subject to secondary transformation, which may affect the accumulation and resources of mercury. The aim of our work is to assess the secondary transformation of organic matter in the soils of drained peatlands of the temperate climate zone and to examine whether it affects mercury resources and profile distribution in organic soils. Field research was conducted in peatlands located in eastern Poland. In the present study, evaluation of secondary transformations occurring after drainage was based on observations of soil morphological characteristics, physical and chemical properties as well as fractional composition of organic matter of the identified soil horizons (to depth 70 cm). Standard cold vapor atomic absorption spectrometry (CV-AAS) was used to measure the total mercury content. In our research, we found a significant effect of the secondary transformation of organic matter occurring in drained peatlands of the temperate climate zone on the total mercury content and stock in soils. The highest content and differentiation of mercury occurred in murshic horizons (up to a maximum depth of 43 cm). The average mercury content of the distinguished soil horizons is grouped in the following series (in μg kg−1): M1 (212.0) > M2 (182.8) > M3 (126.3) > Pt (84.9). The mercury stock, up to a depth of 70 cm in the tested soils, ranged from 17.5 to 39.6 mg m−2. As much as 82.2% of soil mercury was found in the upper murshic horizons. We found strong correlations between soil properties characteristically variable in the secondary transformation process and total mercury content. The increased content of humic substances in murshic horizons caused a significant increase in the total mercury content. Our research is of great importance for soil monitoring, as the amount of determined mercury was greatly influenced by the depth of sampling (up to 25 cm). The results of the research should be taken into account when planning the restoration of peatlands of the temperate climate zone. There is a potential risk that elevated mercury concentrations in the upper murshic horizons may be a source of methylmercury for a long period of time. In peat soils with a high concentration of mercury, the risk of contamination with this toxic metal should be determined before re-irrigation.