Tree biomass and soils (especially organic soils) are significant carbon pools in forest ecosystems, therefore forest management practices, in order to ensure carbon storage in these pools and to mitigate climate change, are essential in reaching climate neutrality goals set by the European Union. Overall studies have focused on diverse aspects of forest carbon storage and greenhouse gas (GHG) fluxes from mineral soils, and recently also from organic soils. However, the information about old-growth forests and the long-term effects of drainage on GHG fluxes of organic soils is missing. Additionally, a large proportion of Scots pine (Pinus sylvestris L.) forests on organic soils in the hemiboreal region are drained to regulate groundwater level and to improve above-ground carbon storage. The study aims to assess the intra-annual dynamics of soil carbon dioxide (CO2) and methane (CH4) fluxes in hemiboreal old-growth Scots pine stands on organic soils with diverse groundwater levels. Six old-growth stands (130–180 years old) were evaluated. In old-growth forests, the main source of soil CO2 emissions is ground vegetation and tree roots (autotrophic respiration), while heterotrophic respiration contributes to almost half (41%) of the total forest floor ecosystem (soil) respiration. The total forest floor respiration and soil heterotrophic respiration are mainly affected by soil temperature, with minor but statistically significant contribution of groundwater level (model R2 = 0.78 and R2 = 0.56, respectively). The CO2 fluxes have a significant, yet weak positive relationship with groundwater level (RtCO2 R2 = 0.06 RhCO2 R2 = 0.08). In contrast, total soil CH4 uptake or release depends primarily on groundwater level fluctuations, with a minor but significant contribution of soil temperature (model R2 = 0.67). CH4 flux has high variability between stands.