Disclosed is a water treatment system including a raw water tank, a module which includes a filtration membrane, a feed pump, a filtered water tank, a backwash pump which flows filtered water backward from the filtered water tank to the module, a valve and a channel which switch the direction of the water flow between the forward and reverse directions, a controller which suspends the supply of raw water from the raw water tank to the module, switches the valve and channel to the reverse direction, makes the backwash pump to supply filtered water from the filtered water tank to the module thereby backwashing the filtration membrane, and washing drainage treatment line including which treats backwashing drainage generated by backwashing of the filtration membrane, and returns the water to the raw water tank.