A model based on the code CrunchClay is presented for a fracture-clay matrix system that takes electrostatic effects on transport into account. The electrostatic effects on transport include those associated with the development of a diffusion potential as captured by the Nernst-Planck equation, and the formation of a diffuse layer bordering negatively charged clay particles within which partial anion exclusion occurs. The model is based on a dual continuum formulation that accounts for diffuse layer and bulk water pore space, providing a more flexible framework than is found in the classical mean electrostatic potential models. The diffuse layer model is obtained by volume averaging ion concentrations in the Poisson-Boltzmann equation, but also includes the treatment of longitudinal transport within this continuum. The calculation of transport within the bulk and diffuse layer porosity is based on a new formulation for the Nernst-Planck equation that considers averaging of diffusion coefficients and accumulation factors at grid cell interfaces. Equations for function residuals and the associated Jacobian matrix are presented such that the system of nonlinear differential-algebraic equations can be solved with Newton’s method. As an example, we consider a 2D system with a single discrete fracture within which flow and advective transport occurs that is coupled to diffusion in the clay-rich matrix. The simulation results demonstrate the lack of retardation for anions (e.g., 36Cl−) of the contaminant plume within the fracture flow system because they are largely excluded from the charged clay rock, while the migration of cations (e.g., 90Sr++) is more strongly attenuated. The diffusive loss of divalent cations in particular from the fracture is accentuated by their accumulation in the diffuse layer within the clay-rich matrix.