Korea Atomic Energy Research Institute’s Post Irradiated Examination Facility safely stores spent nuclear fuel using a wet storage method to conduct research. Here, in order to remove the radioactivity released into the water, the stored water is passed through an ion exchange resin tower, and the radionuclides are exchanged with the bead-shaped ion exchange resin filled inside to lower the radioactivity concentration. At this time, because the stored water passes in one direction, clogging of the ion exchange resin occurs. If this phenomenon continues, the flow rate of the water treatment process decreases and operation efficiency decreases, so a backwashing process is necessary to re-mix the ion exchange resin and secure the flow rate again. In this study, the flow rate reduction trend according to the lifespan of the ion exchange resin and the flow rate recovery according to the backwash process operation amount were analyzed. The flow rate reduction trend of the ion exchange process was analyzed immediately after the backwashing process was started. In addition, the amount of flow recovery according to the backwash process operation amount was evaluated by the amount of waste generated during the backwash process and the number of days of operation until the backwash process was needed again. As a result, the flow rate of the ion exchange process decreased rapidly right after the backwash process until the position of the ion exchange resins was stabilized, and then stabilized. After that, it gradually decreased and reached the point where the backwash process was necessary. However, the decline trend was analyzed to be the same regardless of the lifespan of the ion exchange resin. In addition, the amount of waste generated during the operation of the backwash process was increased in the order of 400 L, 600 L, 1,100 L, 1,400 L, 3,500 L, and 4,200 L to increase the amount of operation of the backwash process. As a result, the number of days of ion exchange resin operation was 285 days, 338 days, and 342 days, was analyzed as 422 days, 322 days, and 720 days. Based on this study, it was confirmed that the flow rate reduction trend is the same regardless of the lifespan of the ion exchange resin, and as the backwash process operation increases, the number of days the ion exchange process can be operated increases, but there is a turning point where the waste treatment cost exceeds the number of days of operation.