Treatment of sludge in sludge treatment reed bed systems includes dewatering and mineralization. The mineralization process, which is driven by microorganisms, produces different gas species as by-products. The pore space composition of the gas species provides useful information on the biological processes occurring in the sludge residue. In this study, we measured the change in composition of gas species in the pore space at different depth levels in vertical sludge residue profiles during a resting period of 32 days. The gas composition of the pore space in the sludge residue changed during the resting period. As the resting period proceeded, atmospheric air re-entered the pore space at all depth levels. The methane (CH4) concentration was at its highest during the first part of the resting period, and then declined as the sludge residue became more dewatered and thereby aerated. In the pore space, the concentration of CH4 often exceeded the concentration of carbon dioxide (CO2). However, the total emission of CO2 from the surface of the sludge residue exceeded the total emission of CH4, suggesting that CO2 was mainly produced in the layer of newly applied sludge and/or that CO2 was emitted from the sludge residue more readily compared to CH4.