The bentonite barrier is an essential part of a safe spent fuel repository in granitic bedrock. One of the most important safety functions of bentonite buffer is to limit groundwater flow so that all mass transport takes place by diffusion. In this work a new mathematical model was developed to define the transport of ions inside the bentonite, where there are bound interlayer water and free extra layer water and sorption capability. This model is tested in a specified geometry and calculated by two numerical platforms—Numerrin and COMSOL Multiphysics—and compared to the original TOUGHREACT model. The model comparison was not a straightforward task because of different approaches in the model setup. Therefore, all the equations are written down, and parameterization is done to create model descriptions near each other. The developed model adapts easily, and there are many new ideas to be tested in bridging the gap between performance assessment and real systems.