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Using microbial fuel cells (MFCs) to power a capacitive deionization (CDI) process enables simultaneous removal of salinity and organic matter in wastewater. The desalination performance of an MFC-CDI system can be influenced by not only the capacity of individual components but also the arrangement and operation of the MFC-CDI circuit. Five typical circuits (consisting of serial- or parallel-connected MFCs or CDIs) and two ion-desorption modes (short-circuit and reverse-voltage desorption) were compared. Results showed that the MFC-CDI system could be reasonably modeled (R² > 0.967) by a first-order resistor–capacitor circuit. The optimal arrangement of the MFC-CDI circuit depended on the electrical characteristics of selected MFCs and CDIs as well as operating conditions. When the system was powered by two MFCs of a larger internal resistance (146 Ω), the highest salt removal after 60 min (m₆₀; 7 …