The nitrates we can get down to acceptable levels with standard flocculation and sedimentation levels. We do regular tests to make sure they aren't over maximum containment levels. Mind you, I wouldn't be terribly happy if a chicken house was directly upstream of my water source. Rivers in general are a pain to draw and treat water from. Like the ol' Greek philosopher said, "you never step in the same river twice". Besides the fact that the river turbidity can change in minutes, you never really know what's coming down the stream at you. Fortunately, our plant draws from a lake, which acts as a giant settling basin.
I've always found it interesting that meat processing plants have to have their own in-house water treatment plants. Granted, they don't have meet the same requirements that a drinking water plant, but you can't just dump all that bloody slurry directly into the sewage system.
Really, a plant operator's biggest fear is getting petrochemicals like gasoline in their water source. The only way to get long chain hydrocarbons out of water is aeration.