Natural fractures are characterized by high internal heterogeneity. This internal variability is the cause of flow channeling, which in turn leads to contaminant transport taking place primarily along the high-velocity channels. Mass exchange between the high-velocity channels and the low-velocity zones has the potential to enhance contaminant retention, due to solute diffusion into the low-velocity zones and subsequent exposure to additional surface area for diffusion into the bordering rock matrix. Here, we derive a random walk particle tracking method for heterogeneous fractures, which includes an additional term to account for the aperture gradient. The method takes into account advection, diffusion in the fracture and matrix diffusion. The developed numerical framework is applied to assess the effect of low-velocity zones in rough self-affine fractures. The results show that diffusion into low-velocity zones has a visible but modest impact on contaminant retention. The magnitude of this impact does not change considerably, regardless of whether diffusion into the rock matrix is considered in the model, and increases for a decreasing average Peclet number of the fracture. Natural fractures are highly heterogeneous, comprising flowing channels and lower-velocity zones We study the effects that diffusion into low-velocity zones has in contaminant transport through rough fractures Accounting for diffusion in low-velocity zones has a relatively modest impact on contaminant retention