A variable water pump control apparatus, may include a detecting portion detecting engine speed, operation of an idle stop and go system (ISG), coolant temperature, operation of a blower, and outside temperature, a variable water pump selectively circulating a coolant through an engine, and a control portion controlling the variable water pump according to the detected information including operating conditions and outside environmental factors, and a variable water pump control method may include detecting a driving condition and an environmental condition of a vehicle, and engaging or releasing a clutch of a variable water pump according to a detected condition so as to selectively circulate a coolant.