I don't think you can, mine do it all the time with no problems, and I wouldn't worry about it unless their is some thing really bad getting in the water (chemicals, etc.).
It's very unhygienic for chickens to do this but if you can figure out a way to stop them could you let me know how you achieved it? Seriously- stagnant water is a menace to their health especially stagnant water that also has poop in it. I have been filling in any holes they make with sand, but they just use the freshly filled holes as new dust bath areas and promptly empty out the holes enough for them to fill back up with water when it rains. Silly birds.
Improving drainage away from run first choice. Second choice is to add a lot of sand to raise ground level and enable water to infiltrate soil better. Digging a couple trenches 6" or so deep in run connecting with low spot outside or down hill slope outside and backfilling with sand may enable better drainage as well.
Thanks. There only 2 small small puddles which are the 2 locations they dug up for a dust bath. I just keep swishing the water out of the run... Sometimes they beat me to it. Just don't know why they do it, it can't taste good...
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I think in nature, based on where ancestors of chickens come from, they are adapted to use stagnant and evaporating bodies of water. Difference is waste collected in run of poultry origin and likely more concentrated, a lot more feces and potentially uneaten feed. Unless number of birds low and run big, I would invest effort in denying birds access to puddles. Simply filling puddles with sand may fix problem for short-term.
They're chickens--it's see water; drink water--I doubt that they taste it. They're just doing what come naturally and, presumably, they have bacteria in their gut that will neutralize any bad microbes. They'll eat their own poop too and pick through manure for fly eggs/larvae--if this bothers you, you're probably keeping the wrong animals. Oh wait, dogs and cats will drink out of the toilet.