Knowledge of the factors that influence the diffusion of contaminants, such as the diffusivity and the connected porosity, is crucial to modeling the long-term fate and transport of contaminants in subsurface systems with small or negligible advective flow, such as in fractured crystalline rock. Fractured rock is naturally heterogeneous, and hence, understanding the diffusivity of a molecule through this material (or the formation factor of the medium) becomes a complex problem, with critical concerns about the scale of laboratory measurements and about the spatial variability of these measurements relative to the scale needed for fate and transport modeling. This study employed both electrical and tracer-based laboratory methods to investigate the effects of scale and pore system connectivity on the diffusivity for volcanic matrix rock derived from the study site, a former underground nuclear test site at Amchitka Island, Alaska. The results of these investigations indicate a relatively well-connected pore system with scale effects generally limited to approximately 6 cm lengths and well-correlated to observed heterogeneous features. An important conclusion resulting from this study, however, is that there is a potential for the estimated diffusivity to be misrepresented by an order of magnitude if multiple samples or longer sample lengths are not used. Given the relatively large number of measurements resulting from these investigations, an analysis of the probability density function (PDF) of the diffusivity was possible. The PDF of the diffusivity was shown to generally follow a normal distribution for individual geologic layers. However, when all of the geologic layers are considered together, the distribution of the subsurface as a whole was shown to follow a lognormal distribution due to the order of magnitude differences amongst the layers. An understanding of these distributions is essential for future stochastic modeling efforts.