You should start by developing an understanding of the contaminents. I think, although the subject matter may be interesting, people are less concerned about detection than using a shotgun approach to removing every possible contaminent 50 times over. I also think electronics will be of little help in detecting biologicals which are probably the main sources of polution.
The usual method of detecting inorganic compounds is to precipitate them out of solution. I see little opportunity for electronics there. You might find interesting projects that will measure the pH, or the alkalinity, or the metalic content.
There is mass spectrometry which is expensive, but probably the most thourough way of analyzing an unknown sample.
I could be wrong on any of these points, this is not my area of expertise. Let us know what you find.