Provided is a method for sterilizing a water treatment apparatus having a plurality of tanks. The method includes, performing a sterilization preparation process to drain purified water from the first tank until a first amount of purified water is left, performing a sterilizing process to sterilize the first tank by supplying the sterilized water supplied from the sterilizing module, to drain water from the first tank through a first water outlet pipe until a second amount of water is left in the first tank, and to drain the second amount of water remaining in the first tank into the second tank through a second water outlet pipe.