Most of the information on soil aggregation and porosity comes from studies of natural soil in which the effects of the different constituents that form the structure overlap. The aim of this research was to study the effects of these constituents separately on well-characterized artificial aggregates in order to understand them better. To do this, the pore system of model silt aggregates, amended with different amounts of humic acids, iron and aluminium hydroxides or colloidal silica, was investigated at three levels of magnification with water vapour desorption (nanometre sizes), mercury intrusion (micrometre sizes) and microtomography (tens of micrometres). Humic acid and aluminium hydroxide increased aggregate porosities measured by all methods. An increase in porosity with increasing additions of each constituent was indicated only by water desorption. We did not observe any well-defined trends in the dynamics of average pore radii. The pore surface fractal dimension determined by mercury intrusion was negatively correlated with that measured by water desorption. The pore system in granular media comprises larger voids joined by narrower necks; therefore, we attempted to relate their sizes with a novel approach that combined microtomography with mercury intrusion and extrusion data. We observed a decrease in the size of pore necks that give access to voids of the same sizes with increasing additions of all constituents. With additions of humic acid this effect was the smallest. The mercury intrusion data showed the formation of separate concretions of iron hydroxides and silica in silt aggregates.