The thermostat was just changed in a 2000 VW Beetle 2.0 lt engine and the shop guy said that the water pump was fine but the thermostat light started flash red again what eles could it be?

It really sounds like the water pump has gone mate.... I have a 200 w 2ltr beelte and the same happened. they changed the termostat and within mins of driving 3 beeps and red light I changed the pump and all is ok, its because they have plastic propellers in them and they crack and stop water being pumped. I paid £90 fitted and all is good. Well I sat that but I still cannot clear the engine check light despite trips to the VW Garage! but that is another story!!