Large areas of northern peatlands have been drained and afforested with conifers in the 20th century. This has led to changes in the hydrology of the peatlands, the quality and quantity of organic matter inputs and soil microbial communities, which are all likely to impact on greenhouse gas (GHG) fluxes. Considerable areas of these forest plantations are undergoing restoration, and our aim was to assess whether contrasting compositions of peat, in conjunction with hydrological changes in a controlled lab experiment, impact on GHG fluxes. We incubated vegetation free cores (at 8 °C) from a near-natural bog, restoration sites felled in 1998, 2006, 2012 and a current forest plantation at (a) low water tables, (b) high tables or (c) water tables that were changed from low to high. Results show that peat quality and nutrient availability in the pore water have been altered by the forest plantations, which resulted in dissimilar carbon dioxide (CO2) fluxes between the sites under the same temperature and water table conditions. Higher CO2 fluxes were found in the peat cores from the forest plantations than from sites that have undergone restoration and from the near-natural bog. However, there were few differences in methane (CH4) fluxes from the different sites, indicating that on its own (i.e., in the absence of biotic interactions under field conditions) the effects of forestry on CH4 flux are limited.