Clean water is one of the main needs in people's life. However, its scarcity has been becoming a major problem. Seawater can be the alternative source for the problem, through desalination system. Previous desalination systems require high cost and energy. One of the low energy technology that can be utilized is the Microbial Desalination Cell, a bioelectrochemical system (BES) and a modified technology of Microbial Fuel Cell (MFC). Modifications of MDC are developed to enhance its performance in desalinating seawater, which one of it is through reactor modification into Stacked Microbial Desalination Cell (SMDC). In this research, the comparison of different reactor configurations on salt removal and desalination rate with tofu industrial wastewater as substrate will be determined. SMDC technology has a focus on cost effectiveness to be applied on large scale. Therefore, the use of modification of the cathode is also applied by using activated carbon as catalyst for oxygen reduction reaction. The result shows that 2-SMDC effectively promote the TDR and buffer phosphate's salt removal performance, which proves to be lower than conventional catholyte, was able to be enhanced by activated carbon coating from 6,86% to 10,93% using optimum AC mass amount of 6 gram.