I grew up on a farm in Iowa so I'm quite familiar with ag runoff. First, what is upstream from you? Hog buildings? Cattle feedlots? Do they apply animal poop as fertilizer upstream from you? How big is the watershed for that stream? Is there anything else in that watershed that could be a polluting source? Is it just cropland?
What does the water look like? Smell it. If it smells like poop, there's poop in it. If an ag operation is letting poop get into the waterways you need to get the DNR involved right now. They will come in and lay wood to any company that's letting poop into the water. I've seen this many times. They will fine the farmer for every single fish, frog, and bird that dies. It can run into the millions.
It might be something natural too. As mentioned, algae blooms can be dangerous. My experience is that dogs usually won't drink bad water like that, but it does happen.
Good luck in finding a solution. If you've got somebody polluting your stream, it needs to be stopped.