Pump  water from the well ...

 Pump  water from the well until you will get a good quality of water, it may take a few weeks depending on the permiability of the ground surrounding the well, send a test sample or make your own test to determine if there are E.coly bacteria ,if so you will need to chlorinate some, before you make it a recharge well please send a sample to the local lab to determine the water are clean , water that still have contaminates can be dangerous and the well can be a source for source for bacteria growth, i suggeset also to cover it with graver so no one will be able to throw things in it and you will still have the infiltration rate needed to recharge the well.