They are a problem in surface water in certain areas. The main agricultural sources would be livestock manure and human sewage that somehow is allowed to enter the surface water. When it gets into surface water, it often kills fish. It is a surface water problem. If water is flowing through the drains, it carries manure to the outlet, where it can cause problems for anything living in the water downstream.
Ammonium is the biggest problem but bacteria and organic matter are also a concern.
The best solution we know of is to break up the soil surface slightly before spreading. An alternative is to spread at times when there is no tile flow. This macro pore flow will not happen to everyone, but it may happen one year when you thought it was never going to be a problem on your farm. At least have a look at your tile outlet when spreading and within the first 24 hours after spreading, to make sure no manure is leaving your property. In an ongoing study of tile water quality on farms representing a variety of management practices, we have measured nitrate levels that are higher for swine farms than for non-livestock farms.