Trough is far away from any foliage so I can rule that out. A quick google and iron staining seems to be the problem. I noticed it first in three new troughs that had been just put in other fields and then a couple of days later noticed mine. I wonder if new pipework could have unsettled things.
Any leaves blowing about? I have willow in my field which blows about and turns the ponies mouths and the water tough black! The buggers love to eat it! Maybe a different leaf would make the red colour?