Flow-electrode capacitive deionization (FCDI) has been studied for its ability to perform continuous deionization; however, there are no reports on the degradation of the desalting performance of FCDI under short-circuited closed cycle operation (SCC) mode. In this study, we observed a gradual decrease in FCDI desalting performance and weight increase of the flow-electrode under SCC mode, which mixes the cathode and anode flow-electrodes. Through an analysis of NaCl and water accumulation rates obtained from the weight variation of the flow-electrode, the gradual decline in the desalting performance was caused by a decrease in the content of activated carbon (AC) with ion adsorption sites in the flow-electrodes. This was driven by water transfer from the feed stream to the flow-electrodes through the ion exchange membrane attributed to hydrated ions and osmosis. We calculated the salt adsorption capacity (SAC) and salt adsorption rate (SAR) based on the variable weight of the flow-electrode. The maximum SAC (mSAC) and average SAR (ASAR) values of the FCDI were higher and lower than those of conventional capacitive deionization systems, respectively. This was likely due to the repetitive use of the flow-electrode and long ion transport pathways in the flow-electrode, respectively.