In deep geological repositories for nuclear waste, the surrounding rock formation serves as an important barrier against radionuclide migration. Multiple potential host rocks contain phyllosilicates, which have shown high efficiency in radionuclide sorption. Recent experimental studies report a heterogeneous distribution of adsorbed radionuclides on nanotopographic mineral surfaces. In this study, the energetic differences of surface sorption sites available at nanotopographic structures such as steps, pits, and terraces are investigated. Eleven important surface sites are selected and the energies of ad- and desorption reactions are obtained from density functional theory calculations. The adsorption energies are then used for the parameterization of a kinetic Monte Carlo model simulating the distribution of adsorbed europium on a typical nanotopographic muscovite surface. On muscovite, silicon step sites are favorable for europium sorption and lead to an increased adsorption in regions with high step concentrations. Under identical chemical conditions, sorption on typical nanotopographic surfaces is increased by a factor of three compared to atomically flat surfaces. Desorption occurs preferentially at terrace sites, leading to an overall 2.5 times increased retention at nanotopographic structures. This study provides a mechanistic explanation for heterogeneous sorption on nanotopographic mineral surfaces due to the availability of energetically favorable sorption sites.