Fresh model cement mixtures, with the same w/c ratio and particle size distribution, were simulated by the SPACE system that is based on a dynamic mixing algorithm. Thereupon, they were hydrated by the HYMOSTRUC 3D system. Boundary conditions were varied, rendering possible assessment of their influence on percolation of capillary porosity by serial sectioning and using the overlap of slices. Simulation results revealed increases in total porosity and in connected fraction of capillary pores due to the existence of aggregate. The de-percolation threshold of capillary porosity was found not only related to total porosity and image resolution, but also governed by the spatial distribution of capillary pores.