There will probably be some compromises worked out, just as there was in a similar case in Idaho several years ago. Part of the problem is that the Kansas laws, that were written to allow the state to enforce the Clean Water Act, have some rather unclear statements. There are also exceptions that contradict the intent of the regulations. There are also a lot of phrases that are not well defined, such as the difference between a farm pond and a fresh water reservoir. Anytime that there is a hard enough rain that you have runoff from any piece of land, there will be some form of pollution or contamination occurring.
Erosion occurs in grasslands.
Simply look at any dry farm pond and see how much silt has washed into it over the years. But the fact that the silt stopped in the farm pond indicates that they are helping to reduce contamination further downstream. When cattle have free access to streams, there is bound to be some waste matter that ends up in that stream. But the same thing can be said for wildlife. These are all reasons why we have water treatment facilities for public drinking water.