Microbial desalination cell (MDC) is a promising technology due to its simultaneous features of electricity production, wastewater treatment, and desalination. In this thesis, boron (B) removal from geothermal water and organic matter removal from yeast wastewater with energy production was studied using a three chamber (anode/desalination/cathode) lab-scale MDC system. Among operational conditions, electrode surface area was proven to be significant on B removal efficiency. Then, anode chamber of the conventional MDC was modified to include three-dimensional (3D) cubic electrodes as a novel design. B and organic matter removal efficiencies and the produced power density results were promising for 3D-electrodes. Further studies in order to increase the efficiency of MDC system was conducted by synthesizing 3D hybrid sponge electrodes with activated carbon-chitosan (AC-CS). MDC with 3D AC-CS anode provided a higher power density of 970 mW/m2 , B removal efficiency of 75.9%, and COD removal efficiency of >90% under optimized conditions. Furthermore, phytoremediation performance of Lemna minor L. on B removal was found to be 96.7 %. Also, removal of B and heavy metals from reverse osmosis (RO) permeate and concentrate streams using RO-MDC hybrid process was studied. The performance of ROMDC system was proven to be significant on B and heavy metals removal efficiency. Lastly, feasibility of B removal from geothermal water using MDC-Donnan dialysis hybrid process was evaluated. The most important output of this study was decreased frequency for pH adjustment. Overall, MDC, being in its early levels of technology readiness, produced promising desalination and energy production results in removal of boron from geothermal brine.