I wouldn't suggest you use the FEV virus on the water supply. It does absolutely nothing for the game and in the long run you end up missing out on a lot of free water.
If you infect the water it would affect the world in such a way that the entire map would need to be altered to take it into account. In the case of using the FEV virus, it will kill all remaining life. As you can imagine, the game wouldn't be much fun if there were no one left to talk to. There is also the fact that the game contains DLC that would be rendered useless based on this decision. Because of this, the decision to use the FEV virus won't really do anything at all. It WILL do something, but you will not get to witness it.
Spoiler time! When you use the virus, you will get a nice cutscene to show how the virus kills everyone and wipes out rivet city. Of course, when you go back to the game, no one has died, there's just a bunch of sick NPCs and that's it. Fairly pointless really. On the other hand, by not using it you are an all-round good guy or gal, and now have access to the aqua pure water that is a handy addition to keep you alive wasteland.