The aggregation and slow migration of nanoparticles in aqueous media have caused serious concerns about their fate and impacts in the subsurface environment. Anthropogenic release and distribution of TiO2 nanoparticles (TNP) have immense potential for surface adsorption, occlusion, impregnation, bioaccumulation, and phase partition into various environmental compartments, and the actual risks in their interactions are still unknown. In an attempt to realize the extent of source zone migration of TNP in a fracture-skin-matrix (F-S-M) medium, a numerical model is developed and analyzed for sensitivity of certain features of the flow field. In addition, the sorptive mass transfer is simulated under four characteristic scenarios with varying assumptions pertaining to the intrinsic heterogeneities. The simulation results highlight the non-selective regulatory role of the skin in providing temporary interfacial space for reversible adsorption between the fracture and the matrix as well as in retarding the desorption rate. A preferential detachment of TNP is observed to be favored by the enhanced properties of skin due to the similarity in diffusion and dispersion coefficients. Out of the four scenarios, the two-site model and two-step model simulated the dynamic pore-filling features of adsorption pertaining to the heterogeneities in TNP and F-S-M characteristics. The results demonstrate that the proposed numerical could fairly detect the transition between local equilibrium and dynamic adsorption-desorption cycles that would eventually determine the mass transfer limitations and the extent of elution of TNP along the flow.