You could get ammonia from organics breaking down, leach fields, spills from unknown sources, upstream water shed area could surprise you what is there.
Ammonia is part of the nitrogen cycle, nitrites, nitrates. It takes different bacterias for each part of the cycle.
Just guessing on what you had there of course, too many variables involved. After having a rain that big, I also assume you have not been having that much before this, could of cleaned up some old vegetation and what else is there.
We use a little bottle with about 5 to 10% ammonia which we use the vapors and not the liquid to look for chlorine gas leaks. It looks like white smoke when chlorine gas gets hit by the ammonia vapor. Does not take much.
You may have heard about people getting sick from a swimming pool like at a motel, where it is enclosed. Some times people who are not familiar with the reactions maybe using a cleaner with a ammonia base. That will make the strong chlorinated water in the pool to gas off.