This research describes the effects of two innovative aqueous polyacrylate polymers on the microstructure of porous stone materials. Such latex nanodispersions have been designed (with and without fluorination) as consolidation agents and tested on two types of sandstone, namely, Prague (Mšené) and Obernkirchen, largely used as building materials for valuable Cultural Heritage objects. Quantitative description of the polymer distribution within the specimens was obtained noninvasively by adopting synchrotron radiation computed microtomography. The propagation-based phase-contrast mode was adopted to test its effectiveness in enabling the recognition of the polymers in the two matrices, which is usually hampered by their low attenuation coefficient for X-rays. Quantitative image analysis revealed significant dissimilarities in total porosity, specific surface area of pores, connectivity density and fractal dimension as a consequence of the consolidation treatments. For instance, about 7% and 3% lower porosity values were found in the consolidated Prague and Obernkirchen sandstones, respectively, with the distribution shifted towards smaller pores. Furthermore, the simulation of water transport, based on the retrieved pore network, evidenced a decrease in water permeability and diffusivity of more than one order of magnitude in the treated samples; the effect was more pronounced along the direction of penetration of the consolidating agent. Overall, both latexes exhibited similar film-forming and pore-filling abilities. In general, the results highlighted the high potential of synchrotron-based 3D X-ray imaging for the quantitative assessments of the porous microstructure of consolidated building materials.