I have seen fecal coli form problems in wells up to 100’ in depth. That particular well was made in gravel from surface to the bottom. No mater how much chlorination was done, the well continued to fail bacteria test. I would say there are special cases where waste could enter the ground water flow and contaminate a highly conductive aquifer. I know for sure there was a huge waste problem a mile up the creek. I would guess that Bob NH is right about bedrock formations being relatively safe from these bacteria, though.
In or area the oilfield has ruined a lot of aquifers. Rural water has been developed and paid for by the big oil companies in these areas.