Knowledge of crystal nucleation and growth is paramount in understanding the geometry evolution of porous medium during reactive transport processes in geo-environmental studies. To predict transport properties precisely, it is necessary to delineate both the amount and location of nucleation and precipitation events in the spatiotemporal domain. This study investigates the precipitation of calcium carbonate crystals on a heterogeneous sandstone substrate as a function of chemical supersaturation, temperature, and time. The main objective was to evaluate solid formation under different boundary conditions when the solid−liquid interface plays a key role. New observations were made on the effect of primary and secondary substrates and the role of preferential precipitation locations on the rock surfaces. The results indicate that supersaturation and temperature determine the amount, distribution pattern, and growth rate of crystals. Substrate characteristics governed the nucleation, growth location, and evolution probability across time and space. Moreover, substrate surface properties introduced preferential sites that were occupied and covered with solids first. Our results highlight the complex dynamics induced by substrate surface properties on the spatial and temporal solute distribution, transport, and deposition. We accentuate the great potentials of the probabilistic nucleation model to describe mineral formation in a porous medium during reactive transport.