I learned something new today - because of your reply. I know that farmers where I live fence off the steams from cattle. So when I got your reply, I “googled” it and found that the farmers/ranchers do it voluntarily. I’m glad to know it is not the EPA.
http://www.gettingmoreontheground.com/2014/03/26/dr-wise-on-livestock-stream-exclusion/
Some States will also give farmers money to build the fence.