In fractured crystalline rocks, contaminants are transported through open fractures by fluid flow and can access the connected pore space of the adjacent rock matrix by diffusion. The mass exchange term between the fracture and the matrix depends on in-plane groundwater flow patterns. Thus, channeling and preferential flow, due to heterogeneity in fracture aperture, have an impact on the overall rock retention capacity. Here, we have used experimental data from the recent Water Phase Diffusion Experiment, carried out at ONKALO (Finland), to assess the influence of channeling on contaminant transport and retention at increasingly larger scales. The upscaling is performed by extracting non-parametric Retention Time Distribution functions from the experimental data and using them to carry out transport simulations along a segmented pathway. The analysis shows that channeling leads to anomalous early breakthroughs at short scales, whereas at increasingly larger distances this effect is smeared out and the nuclide breakthrough curves become mostly controlled by mass exchange processes between the fracture and the matrix. This homogenisation occurs at shorter scales for sorbing nuclides. The influence of channelling on radionuclide retention is shown to be modest due to compensating effects between the shorter groundwater travel times and the larger specific fracture surface area made available through in-plane diffusion into stagnant water. Also, we have shown that the late-time behaviour of the experimental breakthrough curves can be used to infer equivalent parameters that, combined with existing homogeneous-based solutions, provide a good description of contaminant breakthrough curves at larger downstream distances.