In many areas of the world, there is a need to increase water availability. Capacitive deionization (CDI) is an electrochemical water treatment process that can be a viable alternative for treating water and for saving energy. A model is presented to simulate the CDI process in heterogeneous porous media comprising two different pore sizes. It is based on a theory for capacitive charging by ideally polarizable porous electrodes without Faradaic reactions or specific adsorption of ions. A two steps volume averaging technique is used to derive the averaged transport equations in the limit of thin electrical double layers. A one-equation model based on the principle of local equilibrium is derived. The constraints determining the range of application of the one-equation model are presented. The effective transport parameters for isotropic porous media are calculated solving the corresponding closure problems. The source terms that appear in the average equations are calculated using theoretical derivations. The global diffusivity is calculated by solving the closure problem.