Abstract Population growth and increasing global demand for freshwater have raised a serious challenge for the depleting sources of freshwater in the 21st century. Desalination technologies can be a reliable technique for providing freshwater. Capacitive deionization is one of the innovative desalination methods that has received increasing interest. Flow-electrode capacitive deionization (FCDI) (a new architecture of capacitive deionization) is one of the efficient, cost-effective, and environmentally friendly desalination methods for freshwater production. In this experimental research, the performance of an FCDI system was investigated and the influence of important parameters such as flow rate of flow-electrodes, electrolyte salt concentration of flow-electrodes, and initial feed water concentration will be assessed on the efficiency of desalination operation. In this study, the flow-electrodes operated in short-circuited closed-cycle operation (SCC) mode, and also the feed water operated similarly to the flow electrodes in closed cycle. Moreover, in all the experiments, the salt adsorption capacity (SAC) and salt removal efficiency (SRE) was calculated. Herein, by optimizing the above-mentioned parameters, the salt removal efficiency of 83% and a SAC value of 29.12 mg/gdry carbon were achieved in 5 hours.