I'm real late on this topic. This early spring/late winter, I saw the worst liquid manure run-off I have ever seen. In one instance I actually thought a pipe had ruptured: it was that bad, and it ran into an adjacent creek. Fortunately, it did not appear to have killed any fish, but who know about the long-term deleterious results?
I believe this is indeed pollution, and the stench of freshly applied liquid manure is certainly an air pollutant.
But, if a farmer is taken to task for polluting a stream, all he has to do is post his land, contact his neighbors to post theirs, and eventually access to much stream frontage is lost. We really cannot afford to lose any more fishing access.
Yes, I know they do not intentionally pollute streams, that they need the manure for fertilizer -- but pollution episodes happen more frequently than we want to admit. The farmers must do what they can to make a living in this tight economy, and I sympathize with them. But, as time passes in heavily farmed areas, I believe streams are inevitably going to die from the nitrogen pollution from liquid manure run-off. I also believe that the nitrogen and other pollutants will seep into aquifers and pollute them as has happened with the Oglalla Aquifer in the Midwest.
Please do not take this as anti-farming. My wife grew up on a dairy farm, and a number of my friends are hard-working farmers. But, in the area where I live, I am afraid that liquid manure run-off is the number one threat to water quality.