Ideally the water is coming from a free-flowing aquifer. You dig down a few hundred feet. Sometimes the water is sitting on top of the rock. Sometimes it's below. Sometimes it's in a mix of gravel. It could be 100 feet down, it could be 1,000 feet down. It depends on where the water is.

If the water is from an artesian well, it could be coming from a thousand miles away through the bedrock from the mountains. It could be refilled from rain water that leaks down through the water table. It could be from underground streams.

Unless the water is very shallow, there shouldn't be any bacterial contamination. You test the water to see that it's safe to drink. You're looking for bacteria, heavy metals, pesticide runoff, that sort of thing.

My parents well is about 400 feet down. Through the bedrock. The water is from an underground stream and comes up through the cracks in the rock and keeps the field next door always wet, even in a dry year. The water is high in iron but doesn't have heavy metal contamination to speak off. The copper/nickle is closer to the surface in the clay. The clay is full of iron too. At about 6 feet down, the clay has enough iron in it that a magnet sticks to it. Below that, it's a neutral gray clay that goes down to pea gravel, then bedrock. You can get water out of the gravel, but the refill time would be ridiculous so you pull from below it.

All that clay and rock acts like a filter to keep contaminates out of your drinking water.