There are alot of ignorant statements beeing thrown around in this thread. I live in the heart of WNY dairy land, and used to be a dairy farmer, before we sold the cows and became a crop only farm. My local lake has about dozens of large farms in it's watershed, with a 100,000+ cows making manure, and that manure applied to the land that drains into that watershed. Runoff is enevitable, farmers can't controll the weather. Manure needs to be applied to the land for fertilizer, and most farms do it in an environmentaly sound manner. They incorperate it in to the soil ASAP, the don't put it on heavy, if at all next to drains, ditchs, or feeder streams. And they are only allowed to put on a limited amount of manure as dictated by soil needs/run off potential set by there there KAFO plan. Yet runoff still happens.
Since runoff is unavoidable, I would rather have manure, than comercial fert. Manure in the ammounts that runoff now, and now that farmers are educated, and concerned about, is doing little harm. The manure actualy gets used by the lakes biomass, plankton, vegetation, etc...