A method for controlling a water pump of a vehicle moving a coolant circulating through a cooling load generating heat and a radiator includes calculating a rotation speed command based on a control reference temperature of the coolant. A water pump suction pressure is set and compared with a preset control reference pressure to control the rotation speed command. A system for controlling the water pump includes a first temperature sensor for detecting a temperature of a coolant exhausted from the cooling load and a second temperature sensor for detecting a temperature of the coolant to be supplied to the cooling load. A water pump pressure sensor detects a water pump suction pressure, and a water pump driver drives the water pump. A controller controls the water pump driver based on signals received from the first temperature sensor, the second temperature sensor, and the water pump pressure sensor.