Colloid transport in fractured rock formations is an important process impacting the fate of pollutants in the subsurface. Despite intensive and outstanding research on their transport phenomena, the impact of small-scale surface heterogeneity on colloid behavior at the fracture scale remains difficult to assess. In particular, there is relatively little direct experimental evidence on the impact of natural fracture surface heterogeneity on colloid transport. To investigate this, we developed an experimental setup allowing the direct visualization of fluorescent colloid transport, in a flow cell containing a chalk rock sample. We used samples containing both a natural fracture surface and an artificially made smooth surface from the same chalk core. We characterized the roughness and chemical composition of both surface types. From the experiments, we obtained direct images of colloid transport over the surfaces, the colloid breakthrough curves at the outlet of the flow cell, and the residual deposition of colloids on the rock surface. The natural fracture surface exhibited larger physical and chemical heterogeneity than the smooth surface. The aperture variability across the natural fracture surface led to preferential flow and colloid transport, as well as their earlier breakthrough from the flow cell, compared to the artificially made surface. Our experimental setup can be used to further investigate the link between surface heterogeneity, both chemical and physical, on colloid transport and deposition in natural rock fractures.