Membrane capacitive deionization (MCD) technology offers numerous opportunities for water, wastewater treatment, desalination, nutrient removal and recovery and high value-added chemical production. While MCD technology has been explored very well, there are many design-, material- and process-related challenges that pose barriers to their large-scale applications. In this research, we study design parameters such as the distance between the electrodes and membranes, the volume of the anode and cathode compartments and the type of electrode materials that may influence the performance of the MCD process. This study investigates the effect of electrode–membrane distance, novel carbon electrode materials and the type of ion exchange membranes on the efficiency of the MCD process. We test the novel MCD process for the application of desalination across varying concentrations of saline water. We analyze the performance of the system using different initial salt concentrations to assess its ion removal capacity and energy consumption at various electric loads and different process conditions. Key performance indicators such as salt removal efficiency, charge efficiency, and energy per ion removed were evaluated. In addition, we also evaluate the nutrient recovery potential of this novel MCD process. Nitrogen and phosphorous recovery potentials from used hydroponic nutrient water are evaluated using this process. Similar parameters such as the nutrient recovery efficiency, charge efficiency and specific energy consumption of the process are evaluated. The results demonstrate that optimal design of anode and cathode compartments, electrode–membrane distance and sustainable electrode materials may enhance resource efficiency and cost savings.