Ask the Nutritionist: Dr. Getty's Forum for Equine Nutrition
Welcome to my forum.
Here you will find more than 6 years of questions and my answers. It is searchable and offers a great deal of information.
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All the best,
Dr. Getty
Hello Brian,
Excellent question! I have not come across any scientific studies on the subject but I can see your logic. Of course, the amount of chlorine in chlorinated drinking water is very minimal. If it weren't we would suffer from toxicity issues, and it would certainly give us diarrhea because our digestive systems also contain beneficial microbes.
So, I am frankly not overly concerned about it causing a significant reduction of hindgut microbes in the horse's digestive tract. Nevertheless, if the horse develops loose manure, or has an unthrifty appearance, providing a probiotic is a good idea. One like Synbiotic EQ or Equine Gold for the older horse, would be worthwhile.
All the best,
Dr. Getty 
Author of Feed Your Horse Like A Horse
Where are you from? Bayfield, CO