A 3D lattice Boltzmann model is developed and used to calculate the water and gas permeabilities of model cement pastes at different degrees of water saturation. In addition to permeable micron-sized capillary pores and impermeable solid inclusions, the lattice Boltzmann model comprises weakly-permeable nano-porous calcium silicate hydrate (C-S-H). The multi-scale problem is addressed by using an effective media approach based on the idea of partial bounce-back. The model cement paste microstructures are generated with the platform µic. The critical parameters, C-S-H density and capillary porosity, are taken from 1H nuclear magnetic resonance relaxation analysis. The distribution of water and air is defined according to the Kelvin–Laplace law. It is found that when the capillary porosity is completely saturated with a fluid (either water or gas), the calculated intrinsic permeability is in good agreement with measurements of gas permeability on dried samples (10−17–10−16 m2). However, as the water saturation is reduced, the calculated apparent water permeability decreases and spans the full range of experimentally measured values (10−16–10−22 m2). It is concluded that the degree of capillary water saturation is the major cause for variation in experimental permeability measurements. It is further concluded that the role of the weakly-permeable C-S-H, omitted in earlier modelling studies, is critical for determining the permeability at low capillary saturation.