Abstract Saline water such as seawater or brackish water is a potential source for drinking water or for non-potable applications, but the existing desalination techniques are energy intensive. Therefore, there is an urgent need to develop sustainable desalination methods. Microbial desalination cells (MDCs) hold great promise for energy-efficient saline water desalination. In MDCs, electrical energy from wastewater is extracted by taking advantages of microbial extracellular respiration and used to drive desalination. Herein, we have comprehensively reviewed and discussed the potential functions of MDCs, including seawater desalination, brackish water desalination, water softening, hydrogen and chemical production, and groundwater remediation along with wastewater treatment. The role of process parameters in improving the MDC performance was also analyzed. We expect to provide insight into the advantages and limitations of this emerging technology from the aspect of its functions, thereby encouraging more research efforts towards further development and commercialization of MDCs.