The invention relates to a method and apparatus for controlling a water pump for a vehicle. The method includes the steps of determining whether an engine is on; measuring a coolant temperature of the engine and an RPM of the engine when the engine is determined to be operated; determining whether the measured coolant temperature is equal to or greater than a predetermined coolant temperature; determining an RPM of a water pump, which adjusts a coolant flow rate, from the measured coolant temperature and the measured RPM of the engine, when the measured coolant temperature is determined to be equal to or greater than the predetermined coolant temperature; and controlling the water pump such that the water pump is operated according to the determined RPM of the water pump.