A water treatment system includes: EDI having deionization chamber that deionizes water that contains boron and concentration chambers in which concentrated water flows; and a cooler to cool the water supplied to deionization chamber or the concentrated water supplied to concentration chambers. Alternatively, water treatment system includes EDI having deionization chamber that deionizes water that contains boron, concentration chambers in which concentrated water flows, and electrode chambers in which electrode water flows; a cooler that adjusts temperature of the water or temperature of the concentrated water supplied to concentration chamber; and a controller that controls the cooler such that the cooler adjusts the temperature of the water supplied to deionization chamber or the temperature of the concentrated water supplied to the concentration chambers within a range of 10-23° C., based on the temperature of the water, temperature of treated water of EDI, the temperature of the concentrated water, or temperature of the electrode water.