We present an innovative approach that combines a unique real‐time data set documenting absolute dissolution rates of a calcite crystal with an original reactive transport model tailored to the analysis of the dynamics of nano‐scale mineral dissolution processes. Providing robust and physically based fundamental understanding on the kinetics of mineral dissolution is at the core of various geo‐engineered strategies to quantify chemical weathering patterns across diverse spatial and temporal scales. Here, we rely on data obtained through Atomic Force Microscopy. We provide a mathematical framework to describe three‐dimensional dynamics of the mineral surface topography, and show convergence of the numerical approach for vertical grid spacing down to sub‐nm resolution.