Free fecal water syndrome is not the same as diarrhea. With diarrhea, the entire stool is loose or even watery. With free fecal water syndrome, the stool is normal but small amounts of very thin water with a small amount of feces are passed before, after or during defecation. And although this does not seem like a major problem, some horses have enough of this free fecal water to pollute the tail and legs, and it can be severe enough to cause skin lesions. This material on the legs and tail also attracts flies and makes it very difficult to keep these horses clean.

Although not a common problem, the condition occurs enough that it has been blamed on many different factors with no proof of any actual cause. Some possibilities for the problem include feeding alfalfa hay, feeding haylage or silage, drinking very cold water, poor dental care, and parasites. Also, various nutritional supplements are marketed to prevent this problem because it seems there is a nutritional supplement marketed to cure every horse problem whether there is any proof the supplement is effective or not.

To try and learn more about the condition, a study was performed in Germany and it found that the condition more likely occurred in horses that had a low rank in a group of horses. Also, the condition was more common in horses in the winter as it was believed the subordinate horses were confined in a smaller space, which leads to more anxiety. Dental disease, parasites and cold water intake was shown to not be related to the condition. Geldings are more commonly affected than mares as mares are usually more dominant than geldings. Paint horses are also more commonly affected.