A method for operating a membrane separation device of a water treatment facility for performing solid-liquid separation of water to be treated via a separation membrane, the water treatment facility comprising: a first water tank in which the membrane separation device is immersed; a second water tank comprising an oxygen-free tank filled with activated sludge and an aerobic tank which has a diffuser installed at a bottom thereof and in which ammoniac nitrogen contained in the water to be treated is nitrified into nitrate nitrogen, the second water tank being in communication with the first tank such that a water level thereof is the same as that of the first water tank; a third water tank into which overflowing water from the first water tank is flowing; and a membrane filtration control unit, the method comprising: a membrane filtration process for setting a flow amount M(t) of permeated water from the membrane separation device so as to satisfy a relationship expressed by the following equation: M(t) = KQ(t-1), where M(t) is a flow amount of the permeated water during a time period t having a predetermined length, K is a gain (> 1), and Q(t-1) is an amount of inflow of the water to be treated into the second water tank during a time period t-1 immediately prior to the time period t, and extracting the permeated water from the membrane separation device by the set flow amount M(t) of the permeated water by a first pump controlled by the membrane filtration control unit; and a halt process for temporarily stopping the extracting the permeated water from the membrane separation device when a water level of the third water tank becomes lower than a predetermined halt water level, wherein excessive activated sludge contained in the water to be treated which overflows into the third water tank disposed adjacent to the first water tank is returned to the second water tank together with nitrate nitrogen contained in the water to be treated by a second pump, which is reduced to nitrogen by denitrification and part of which is extracted and discarded, and wherein a return amount of the activated sludge is set to about 4 times with respect to a design inflow amount of the water to be treated. a first water tank in which the membrane separation device is immersed; a second water tank comprising an oxygen-free tank filled with activated sludge and an aerobic tank which has a diffuser installed at a bottom thereof and in which ammoniac nitrogen contained in the water to be treated is nitrified into nitrate nitrogen, the second water tank being in communication with the first tank such that a water level thereof is the same as that of the first water tank; a third water tank into which overflowing water from the first water tank is flowing; and a membrane filtration control unit, the method comprising: a membrane filtration process for setting a flow amount M(t) of permeated water from the membrane separation device so as to satisfy a relationship expressed by the following equation: M(t) = KQ(t-1), where M(t) is a flow amount of the permeated water during a time period t having a predetermined length, K is a gain (> 1), and Q(t-1) is an amount of inflow of the water to be treated into the second water tank during a time period t-1 immediately prior to the time period t, and extracting the permeated water from the membrane separation device by the set flow amount M(t) of the permeated water by a first pump controlled by the membrane filtration control unit; and a halt process for temporarily stopping the extracting the permeated water from the membrane separation device when a water level of the third water tank becomes lower than a predetermined halt water level, wherein excessive activated sludge contained in the water to be treated which overflows into the third water tank disposed adjacent to the first water tank is returned to the second water tank together with nitrate nitrogen contained in the water to be treated by a second pump, which is reduced to nitrogen by denitrification and part of which is extracted and discarded, and wherein a return amount of the activated sludge is set to about 4 times with respect to a design inflow amount of the water to be treated. a membrane filtration process for setting a flow amount M(t) of permeated water from the membrane separation device so as to satisfy a relationship expressed by the following equation: M(t) = KQ(t-1), where M(t) is a flow amount of the permeated water during a time period t having a predetermined length, K is a gain (> 1), and Q(t-1) is an amount of inflow of the water to be treated into the second water tank during a time period t-1 immediately prior to the time period t, and extracting the permeated water from the membrane separation device by the set flow amount M(t) of the permeated water by a first pump controlled by the membrane filtration control unit; and a halt process for temporarily stopping the extracting the permeated water from the membrane separation device when a water level of the third water tank becomes lower than a predetermined halt water level, wherein excessive activated sludge contained in the water to be treated which overflows into the third water tank disposed adjacent to the first water tank is returned to the second water tank together with nitrate nitrogen contained in the water to be treated by a second pump, which is reduced to nitrogen by denitrification and part of which is extracted and discarded, and wherein a return amount of the activated sludge is set to about 4 times with respect to a design inflow amount of the water to be treated.