According to the USGS website, "The National Water-Quality Assessment Program (NAWQA) provides an understanding of water-quality conditions and how those conditions may vary locally, regionally, and nationally; whether conditions are getting better or worse over time; and how natural features and human activities affect those conditions."
There is a ton of information here about NAWQA, including some links to research about chemicals found in source water. USGS calls this program SWQA, for Source Water Quality Assessment. The source water program is interesting because they are looking at the water that's flowing IN the water treatment plants, as well as the water that is leaving the plants. So far they have found a lot of chemicals surviving the treatment process. However, they stress that many of the chemicals they are looking for are unregulated, and often found in very low doses that don't have known consequences to the end user. They also delve into the various ways the study could have been flawed (ex. how can you be sure you are testing the same water at both ends of the treatment plant?).
From my limited conversations with people who look at stream water quality and people who look at water treatment processes, it sounds like there isn't a lot of communication between the two groups. It would seem logical that the two groups would have a lot of information to share, or at least compare. This gets into one of my pet peeves, actually. We seem to exert a lot of energy chasing after answers that someone else has already caught. That said, I know how easy it is to be busy trying to be productive and not have the leisure time to go listen to someone else talk about what they've been up to. And, I suppose there are times when we want the same information, but in a different context.