A microbial desalination cell (MDC) uses exoelectrogenic bacteria to oxidize organic matter while desalinating water. Protons produced from the oxidation of organics at the anode result in anolyte acidification and reduce performance. A new method was used here to mitigate anolyte acidification based on adding non-buffered saline catholyte effluent from a previous cycle to the anolyte at the beginning of the next cycle. This method was tested using a larger-scale MDC (267 mL) containing four anode brushes and a three cell pair membrane stack. With an anolyte salt concentration increased by an equivalent of 75 mM NaCl using the catholyte effluent, salinity was reduced by 26.0 ± 0.5% (35 g/L NaCl initial solution) in a 10 h cycle, compared to 18.1 ± 2.0% without catholyte addition. This improvement was primarily due to the increase in buffering capacity of the anolyte, although increased conductivity slightly improved performance as well. There was some substrate loss from the anolyte by diffusion into the membrane stack, but this was decreased from 11% to 2.6% by increasing the anolyte conductivity (7.6 to 14 mS/cm). These results demonstrated that catholyte effluent can be utilized as a useful product for mitigating anolyte acidification and improving MDC performance. © 2013 American Chemical Society.