A friend of mine had that problem. They were getting violently sick from surface contamination. They abandonded their well and drilled a new one. I’m sure that’s what you wanted to hear.
You do not even want to bathe in it if it’s contaminated. Ecoli is no joke. This is not going to be inexpensive. But your family’s health is at stake.
Other than that you will have to treat your well water like surface water. A whole house Reverse Osmosis system may do the trick. You may need to couple it with some sort of disinfectant, Chlorine, UV, Ozone. UV may be the ticket on a small scale. I’ve seen UV systems for large saltwater aquariums and not too terribly expensive. I would couple a RO system with a UV system following it. That may do the trick.