In regards to the drinking water. Most water treatment plants now days use a membrane filter which looks like long strands of spaghetti that is pores. The water is drawn threw these and is only the beginning of a long line in treating the water. These water treatment plants remove down to the virus levels. E-coli is naturally in water along with all other pathogens that will make you sick. These treatment plants filter all this out (minus the hormones). You wouldn't notice any difference in your water from last week. These systems are that good. It's just a mind over matter type thing. It's clean water but, now you know what was in it.
Being that it was the Pigeon river I rarely fish it but, had it been the little river I wouldn't worry about fishing it as soon as the river came down to a suitable level. The only ill effects that I could see after the current river flow decreased might be cosmetics actually. You MAY see some inorganic like a stated earlier. The fish should be just fine and I would be truly shocked if there were any fish killed. I can't say that the river would be 100% e-coli free but, I couldn't have said that before the breech.