We present here a new model, CrunchClay, that simulates multicomponent diffusion of ions through clay and clay-rock by taking into account the charge and transport characteristics of the electrical double layer (EDL). The model can be applied in 2-D to clay systems with heterogeneous distributions of mineralogical and surface charge properties. The model makes use of a set of newly developed routines that calculate accurately the fluxes between adjacent grid cells with differing charge properties. In addition, the model is able to consider time-dependent EDL lengths (or volumes) resulting from salinity changes. The more common use of the model, however, is to simulate ion transport through heterogeneous clay rocks, where the distribution of minerals and connected porosity is derived from microtomography or other means. The model is based on a global implicit solve of the reaction-diffusion equation with explicit consideration of two co-existing continua: a bulk water continuum and an EDL continuum in which electrostatic effects are treated. The global implicit or fully coupled approach, while requiring additional software development, offers the advantage of improved computational efficiency and convergence characteristics over operator split treatments of the diffusion-reaction equation. The model is used to simulate uphill diffusion of radiolabeled tracers as well as a reactive and non-reactive tracer in Opalinus Clay.