My best guess is that the clicking you hear is the pressure switch. I assume your water pump is in the well or you would hear more than a clicking noise. Each click you hear is the starting and stopping of the pump. The fact that the clicks are close in time, 2 -3 minutes I will say the pump is losing pressure for some reason. There may be a leak in the line but more likely the check valve in the pump is likely not holding. If the water is not running anywhere the pump and pressure switch should not cycle more than once. If the pressure tank in the basement is working properly the pump should only cut in after running the water for about 5 minutes and should only run for a couple of minutes to build the pressure again. There are other possibilities as well. I recommend you call a plumber to have a look before your pump burns out. It is also possible that the switch settings are set too close together.