Any time you open and work on a well you can introduce bacteria from your hands and equipment.
I would pour a 1 gal jug of Clorox into the well and let it stand overnight and then pump out the water through the equipment you will be using.
Keep pumping till you don't smell the clorox and then get the water tested within the week.
You have an artesian well in which the static water level is higher than the water entry zone into the borehole.
Im assuming this well is drilled into bedrock and that there is casing socketed into the top of rock by the driller.