The 3D description of the soil structure at the pore scale level can help to elucidate the biological functioning of soil. The water-air distribution in the 3D-pore space is of particular interest because it determines the diffusion pathways of nutrients and the localisation of active soil microorganisms. We used the Shan-Chen interparticle-potential approach to simulate spontaneous phase separation in complex academic and real 3D-porous media using the advanced TRT lattice Boltzmann scheme. The equation of state and phase diagram were calculated and the model was verified using hydrostatic laws. The 3D pattern of water/air interface in two complex academic pore geometries was accurately computed. Finally, 3D maps of static liquid-gas distribution were simulated in a real 3D X-ray computed tomography image obtained from an undisturbed soil column sampled in a silty clay loam soil. The simulated soil sample of 1.7 cm(3) was described at a voxel-resolution of 60 mu m. The range of the simulated saturations (from 0.5 to 0.9) was in a good agreement with the expected saturations calculated from the phase diagram.