Investigations of mineral surface reactivity have recently challenged the classical approach of determining dissolution rates from mineral powders as crystals often exhibit heterogeneous and/or anisotropic reactivity. However, face-specific measurements are restricted to small areas at the surface and limited depth and ignore the contribution of the crystal edges to the whole process. Here, we provide a detailed characterization of the dissolution kinetics at pH 4.0 of a single calcite crystal in 3D using X-ray microtomography with a resolution less than 1 μm. The imaging method allows 3D mapping of the crystal surface topography, providing a description of the time-dependent local dissolution fluxes all over the crystal surface, and the calculation of the crystal dissolution rates. The global rate determined at the crystal scale integrates the contribution of all the crystal features, including the faces, edges, and corners, which can be detailed in the local rate distributions. Under acidic conditions, pits develop at the {101̅ 4} surface before dissolution tends to smooth out both the crystal surface asperities and the edges and corners. In addition, a high rate variability is noticed over the crystal surface. The heterogeneous dissolution rates at the crystal surface first led to a local increase of the surface roughness due to pit formation and coalescence, followed by a decrease of the global crystal roughness due to smoothing of the large-scale surface asperities, crystal edges, and corners. Etch pits dominate initially the surface topography, whereas the evolution of the crystal morphology is dominated by the reactivity of edges and corners, whose contribution to dissolution is on average 1.7−3.6 times higher than that of the crystal faces. These results suggest that the dissolution reaction preferentially occurs at the crystal edges and corners, something not considered in most studies of mineral dissolution.