There really isn't an effective way to mark contaminated sources because:
The nasty viruses don't live long - a matter of days, usually - in the environment. Where you'll hit nasty viral contamination, it's because someone upstream from you did something they shouldn't: defecated on the surface, put a cathole close to water or dug one too shallow so that animals spread the material, or defecated or bathed in a stream. Since that can happen anywhere, there's no ready way to list contaminated sources. The presence of dense and undisciplined human populations is a clue, I suppose. But waterborne viruses aren't much of a worry - you're much more likely to get something in your food from another hiker's unwashed hands.
Bacteria are much more of a worry, but every treatment method deals well with them.
Protozoa can be almost anywhere in backcountry water because they have a significant animal reservoir - beavers, in particular, are often implicated. Filtration removes them effectively. Aqua Mira is less effective, but good enough that I use it.
Chemicals - there are a couple of streams from 'hot spots' in Pennsylvania. They're marked. Aside from that, I avoid water from the Surebridge and Doodletown brooks in Harriman because it tastes vile - it surely contains transition-metal salts, although I couldn't say if the levels are worrisome. Otherwise, there are few worries; for the most part, the trail doesn't go downstream of mines.
What do I do? Filter if the temperatures are warm enough that I don't worry about my filter freezing. Aqua Mira in colder weather or if I'm really trying hard to cut the pack weight.