In this study, a model is developed in COMSOL to investigate the nature of energy losses in ion exchange membranes used in electrochemical energy conversion. By use of electrochemical impedance spectroscopy, the nature of resistance and reactance, and therefore the nature of Ohmic resistances and charge transfer resistances, are evaluated. This is done by first obtaining a model of the setup and the resulting impedance spectrum and then making adjustments in the model to observe the impact on the impedance spectrum as well as the resulting ion concentration profiles. In the used system, the diffusion effects were dominant compared to the double layer effects. Therefore, the impedance spectrum is mainly shaped by the diffusion boundary layer, especially at low frequencies. The ion concentration, diffusion coefficients, and membrane properties were found to have a significant influence on the impedance spectrum. Insights from this study can be used in the optimization of ion exchange membranes and the efficiency of energy conversion systems.