I grew up hiking in the shadow of coal country, steel manufacturing, and other assorted heavy industries where you just assume every creek and river is a super fund site. So I usually pack all the water I'll need and plan hikes around my capacity to carry water from my house.
There appear to be a ton of great portable products on the market for filtering parasites, bacteria, and other organic material (e.g. Sawyer). But if you read the fine print, they explicitly say stuff like heavy metal is no bueno.
Some mine runoff is very obvious as the entire creek will be rust colored and burn your skin. There is a creek near by that I shit you not looks as if the Kool-Aid factory went all Willy Wonka with the Blue Raspberry Lemonade flavor.
But even if the water looks clear or at least just regular pre-industrial muddy, I'm hesitant to rely on most filters to top up my bottle.