Heterogeneities of diffusion properties are likely to influence the effective matrix diffusion coefficient determined from tracer breakthrough curves. The objectives of this study are (1) to examine if it is appropriate to use a single, effective matrix diffusion coefficient to predict breakthrough curves in a fractured formation, (2) to examine if a postulated scale dependence of the effective matrix diffusion coefficient is caused by heterogeneity in diffusion properties, and (3) to examine whether multirate diffusion results in the previously observed time dependence of the effective matrix diffusion coefficient. The results show that the use of a single effective matrix diffusion coefficient is appropriate only if the interchannel and intrachannel variability of diffusion properties is small. The scale dependence of the effective matrix diffusion coefficient is not caused by the studied types of heterogeneity. Finally, the multirate diffusion process does not result in the time dependence of the effective matrix diffusion coefficient.