I'd say that the probability of chicken litter affecting water quality is 100%. If you put limiting nutrients into a stream network, it eutrophicates, no question about it. It sounds like the question is, how great is the affect (and what is it) in the cold-water reaches downstream from the dam. Even though the effects pathway is obvious, it can sometimes be rather difficult to prove "harm" by statistically valid measurements of some parameter(s).

This "give me the proof" syndrome with regard to stream issues is something that I deal with professionally on a regular basis. The naysayers know that you will have to expend large amounts of money and time to provide the statistically valid proof. If you do find a way to demonstrate causation and "harm", they claim that more study is needed. This game was played endlessly with salmon issues in the northwest.

I like the kind of approach that Andrew mentioned, the price of proper disposal of wastes should ultimately be included in the purchase price of the product. -- Rick