Microbial desalination cell (MDC) is a new bio-electrochemical technique which converts chemical energy into electrical energy, and at the same time desalinates water and treats wastewater. In this study, MDC performance and water biofouling conditions were tested as an efficient pretreatment desalination process of reverse osmosis (RO). The experiments were designed in a three-chamber reactor to compare the performance of batch and continuous fed modes, using bio-cathode and synthetic wastewater in four different hydraulic retention times and 17 and 35 g/L NaCl concentrations. According to the results, maximum salt removal of about 52.3% was obtained in the continuously fed MDC at 35 g/L NaCl concentration. The maximum salt removal at 17 g/L NaCl was also observed in continuous mode. The anolyte pH in both batch and continuous modes dropped from 7 to 6.32, 6.47 and 6.37, 6.48 in 17 and 35 g/L NaCl concentrations respectively. The chemical oxygen demand (COD) removal values in the continuous mode were 61 and 65% in the anolyte and catholyte respectively, higher than those of fed-batch MDC. The biofouling of the middle chamber solution was confirmed by conducting bio-microbial tests. Our results suggest that the type of hydraulic flow can improve the performance of MDC in different concentrations of NaCl.