A lot of the man-made pollutants that get into the water are not toxic per se, but do things like cause cancer. Sometimes the Clean Water Act levels are in fact too tolerant.
Arsenic is a big one that was underestimated. A while back, the UN put a bunch of well in Bangladesh (?) to prevent cholera or something similar. It worked great. However, there was a lot of arsenic in the water from the wells. They eventually noticed severe health problems due to arsenic. It served as a real wake-up call. Acceptable arsenic levels will be changing in 2006, mostly because of a bunch of dead (and dying) Bangladeshis.
Arsenic builds up in your system, essentially never leaves, so you can drink relatively clean water that will eventually kill you. A lot of the other inorganic (mineral) contaminants, like nitrates, do things like cause cancer.
You have to be careful with things like chlorine too. The halides (of which chlorine is a member) react with organics, like leaf pigment, to make carcinigens and other nasties. You basically have to run it through activated carbon to remove the producs of disinfection.
I'd almost rather just contend with the biologics (germs) like our forefathers did. There is something a little less frightening about fighting bugs that can be killed or filtered outright.
Clean water is really a complicated business nowadays.
Scott