Reactive transport modeling (RTM) is an essential tool for the prediction of contaminants’ behavior in the bio- and geosphere. However, RTM of sorption reactions is constrained by the reactive surface site assessment. The reactive site density variability of the crystal surface nanotopography provides an “energetic landscape”, responsible for heterogeneous sorption efficiency, not covered in current RTM approaches.  Here, we study the spatially heterogeneous sorption behavior of Eu(III), as an analogue to trivalent actinides, on a polycrystalline nanotopographic calcite surface and quantify the sorption efficiency as a function of surface nanoroughness. Based on experimental data from micro-focus time-resolved laser-induced luminescence spectroscopy (µTRLFS), vertical scanning interferometry, and electron back-scattering diffraction (EBSD), we parameterize a surface complexation model (SCM) using surface nanotopography data. The validation of the quantitatively predicted spatial sorption heterogeneity suggests that retention reactions can be considerably influenced by nanotopographic surface features. Our study presents a way to implement heterogeneous surface reactivity into a predictive SCM for enhanced prediction of radionuclide retention.