Laboratory columns under continuous flow were packed with peat from the catotelm of an ombrotrophic bog to simulate the natural environment. Methane concentration increased from 1.4 to 47.8 μmol ml−1due to anaerobic microbial degradation of the peat, while at the same time the water flow rate decreased from log ‐1.39 to ‐3.03 cm3s−1and the moisture content decreased from 85.7 to 56.6%. A control column sterilized by irradiation produced carbon dioxide, but, as the flow of water washed this soluble gas out of the column, the hydraulic conductivity and moisture content increased. These two results suggest that it is the volume of the gas (in the gas phase within the bog) that controls the hydraulic conductivity of peat bogs. Volume accounting at the end of the experiment showed no gas in the sterilized column but 17% gas by volume in the microbially active column. We suggest that as gas bubbles occlude the interstitial pores of the peat the water flow is impeded, reducing both the hydraulic conductivity and the water saturation. The difficulty experienced in draining peat bogs is due to this occlusion, which is also responsible for the heightened water table found in raised bogs. Although methane is produced in bogs, only very low levels of methane emission have been reported. Thus the methane released from northern areas will only significantly contribute to increasing radiative gases in the atmosphere if the bogs themselves are disturbed, for example by mining, when the entrapped methane is released, the water table falls, and the bog dries out.