a b s t r a c tMicrobial desalination cells (MDCs) taking advantage of energy in wastewater to drive desalination represent a promising approach for energy-efficient desalination, but concerns arise whether contaminants in wastewater could enter the desalinated stream across ion exchange membranes. Such back diffusion of contaminants from the anolyte into the desalinated stream could be controlled by two mechanisms, Donnan effect and molecule transport. This study attempted to understand those mechanisms for inorganic and organic compounds in MDCs through two independently conducted experiments. Donnan effect was found to be the dominant mechanism under the condition without current generation. Under open circuit condition, the MDC fed with 5 g L À1 salt solution exhibited 1.9 ± 0.7%, 10.3 ± 1.3%, and 1.8 ± 1.2% back diffusion of acetic, phosphate, and sulfate ions, respectively. Current generation effectively suppressed Donnan effect from 68.2% to 7.2%, and then molecule transport became more responsible for back diffusion. A higher initial salt concentration (35 g L À1 ) and a shorter HRT (1.0 d) led to the highest concentration gradient, resulting in the most back diffusion of 7.1 ± 1.2% and 6.8 ± 3.1% of phosphate and sulfate ions, respectively. Three representative organic compounds were selected for test, and it was found that organic back diffusion was intensified with a higher salt concentration gradient and molecular weight played an important role in compound movement. Principal component analysis confirmed the negative correlation between Donnan effect and current, and the positive correlation between molecule transport and concentration gradient related conditions.