In this study, the operating conditions of a membrane capacitive deionization (MCDI) system were optimized to enhance the desalination rate and water recovery (WR). To improve WR, an intermittent flow mode (IFM) was implemented in the system; the mode comprised a pause step (solution supply interruption) and flush step (solution supply resumption), during desorption. Optimal desorption conditions were determined through desorption experiments by considering pause time (PT) and flush time (FT). Additionally, adsorption was conducted at various current densities by controlling the total adsorption charge below the maximum allowable charge (MAC). The desorption rate (discharge rate) exhibited no significant difference when desorption was performed with or without solution supply to the MCDI cell. Analysis of the discharge rate during the pause step indicated that it was desirable to set the PT to discharge approximately 90% of the total charge accumulated in the carbon electrode. Furthermore, as FT decreased, WR increased, and the residual charge on the carbon electrode increased. Consequently, during adsorption, the cell potential increased, leading to electrode reactions. On the other hand, by increasing the current density while keeping the supplied charge to the cell below the MAC value, it was confirmed that electrode reactions did not occur, even at a cell potential of approximately 3.0 V. Increasing the current density correspondingly increased the desalination rate and salt removal efficiency, but it decreased WR.