We assessed total mercury (THg) concentrations and greenhouse gas (GHG) emissions in pristine and managed hemiboreal peatlands in Latvia, aiming to identify environmental factors that potentially affect their variation. The THg concentrations in soil ranged from <1 µg kg−1 to 194.4 µg kg−1. No significant differences between THg concentrations in disturbed and undisturbed peatlands were found, however, the upper soil layer in the disturbed sites had significantly higher THg concentration. During May–August, the mean CO2 emissions (autotrophic and heterotrophic respiration) from the soil ranged from 20.1 ± 5.0 to 104.6 ± 22.7 mg CO2-C m−2 h−1, N2O emissions ranged from −0.97 to 13.4 ± 11.6 µg N2O-N m−2 h−1, but the highest spatial variation was found for mean CH4 emissions—ranging from 30.8 ± 0.7 to 3448.9 ± 1087.8 µg CH4-C m−2 h−1. No significant differences in CO2 and N2O emissions between disturbed and undisturbed peatlands were observed, but CH4 emissions from undisturbed peatlands were significantly higher. Complex impacts of environmental factors on the variation of THg concentrations and GHG emissions were identified, important for peatland management to minimize the adverse effects of changes in the biogeochemical cycle of the biophilic elements of soil organic matter and contaminants, such as Hg.