Methods for improving ion flux and energy efficiency in a membrane stack of an electrodialysis unit wherein the membrane stack is disposed between an anode and a cathode each in an electrolyte of a selected concentration. Methods include increasing the concentration of the electrolyte, adding a strong base to the electrolyte and adding buffering anions to the electrolyte. Methods for cleaning the electrodes of such a unit involving involve applying a pulsed polarity reversal to the electrodes. Also provided are methods for improving unit operation by increasing the basicity of the electrolyte to the anode and increasing the acidity of the electrolyte to the cathode or alternatively or in addition, by applying heat to increase the operating temperature of at least one of the electrolyte and the treated water stream.