This review examines the interactions between soil physical factors and the biological processes responsible for the production and consumption in soils of greenhouse gases. The release of CO2 by aerobic respiration is a non-linear function of temperature over a wide range of soil water contents, but becomes a function of water content as a soil dries out. Some of the reported variation in the temperature response may be attributable simply to measurement procedures. Lowering the water table in organic soils by drainage increases the release of soil carbon as CO2 in some but not all environments, and reduces the quantity of CH4 emitted to the atmosphere. Ebullition and diffusion through the aerenchyma of rice and plants in natural wetlands both contribute substantially to the emission of CH4; the proportion of the emissions taking place by each pathway varies seasonally. Aerated soils are a sink for atmospheric CH4, through microbial oxidation. The main control on oxidation rate is gas diffusivity, and the temperature response is small. Nitrous oxide is the third greenhouse gas produced in soils, together with NO, a precursor of tropospheric ozone (a short-lived greenhouse gas). Emission of N2O increases markedly with increasing temperature, and this is attributed to increases in the anaerobic volume fraction, brought about by an increased respiratory sink for O2. Increases in water-filled pore space also result in increased anaerobic volume; again, the outcome is an exponential increase in N2O emission. The review draws substantially on sources from beyond the normal range of soil science literature, and is intended to promote integration of ideas, not only between soil biology and soil physics, but also over a wider range of interacting disciplines.