Capacitive Deionization (CDI) is an electrochemical method for water desalination employing porous carbon electrodes. To enhance the performance of CDI, identification of electronic and ionic resistances in the CDI cell is important. In this work, we outline a method to identify these resistances. We illustrate our method by calculating the resistances in a CDI cell with membranes (MCDI) and by using this knowledge to improve the cell design. To identify the resistances, we derive a full-scale MCDI model. This model is validated against experimental data and used to calculate the ionic resistances across the MCDI cell. We present a novel way to measure the electronic resistances in a CDI cell, as well as the spacer channel thickness and porosity after assembly of the MCDI cell. We identify that for inflow salt concentrations of 20 mM the resistance is mainly located in the spacer channel and the external electrical circuit, not in the electrodes. Based on these findings, we show that the carbon electrode thickness can be increased without significantly increasing the energy consumption per mol salt removed, which has the advantage that the desalination time can be lengthened significantly.