Desalination technologies can increase potable water supplies worldwide. One possible approach, capacitive deionization (CDI), could prove optimal for brackish water treatment. At present, CDI development has largely focused on increasing salt adsorption capacity and desalination rates of materials and devices. In addition to these metrics, ultimately, optimizing salt rejection and throughput will be essential. In this work, we present a framework for the design of flow-between CDI cells for maximum salt rejection. We developed a model that is dependent on device specific parameters (system volume, flow rate, inlet and outlet water quality), to generalize the design of a cell for any given requirement. We showed that decreasing the advection-diffusion Peclet number and increasing the aspect ratio of the electrode compared to the channel space yield the highest salt rejection. In addition, tuning the cycle frequency time for salt rejection instead of complete electrode charging can yield faster water production rates and optimal salt rejection. These modeling results were validated through experimental prototypes that made use of vertically-aligned carbon nanotube (VA-CNT) electrodes. This framework to maximize salt rejection can be extended to a multitude of porous electrodes used in flow-between CDI devices.