A significant challenge in contaminant transport modeling is to obtain a mechanistic understanding of transport parameter scaling that accurately addresses the combined influence of physical and chemical heterogeneities at different scales. In this paper, we have developed a scaling methodology to upscale matrix sorption coefficients for fractured-rock systems by characterizing both the tortuosity field (physical heterogeneity) and retardation factor field (chemical heterogeneity) in the rock matrix. We compute the effective tortuosity with a conservative tracer (e.g., tritium), and then using a sorbing tracer (e.g., uranium), we derive the equations for upscaling the sorption coefficients in a saturated, fractured rock system. The derived upscaling equations for the sorption coefficients are verified with Monte Carlo simulations, which are based on a generalized dual-porosity model to enable highly efficient and accurate numerical simulations of diffusive concentration fronts moving between the fractures and matrix material. The scientific results from this study will provide a theoretical and practical link between controlled experimental results at scales increasing from the laboratory bench to the field scale at which risk assessment and contaminant remediation are actually conducted.