Loose manure in horses most often traces back to a disruption in the hindgut, where billions of microbes ferment fiber and regulate water absorption. The cause can be as simple as a sudden feed change or as serious as a bacterial infection. Understanding which category your horse falls into helps you decide whether to adjust management or call a vet.
Too Much Starch Reaching the Hindgut
Horses digest starch primarily in the small intestine, but there’s a limit to how much it can handle. When a horse eats a large grain meal or a concentrate high in starch, the excess passes undigested into the large intestine. There, acid-producing bacteria (especially lactobacilli and streptococci) feast on it, multiplying rapidly while the fiber-fermenting bacteria that normally dominate the hindgut decline. The result is a drop in pH, a condition called hindgut acidosis, which irritates the intestinal lining and draws water into the gut. That excess water loosens the manure.
This is the same mechanism behind loose stools after a sudden forage change. Switching from one type of hay to another, turning a horse out on lush spring pasture, or dramatically increasing grain without a gradual transition all shift the microbial balance faster than the gut can adapt. The general rule is to make any feed change over 7 to 14 days, increasing the new feed by no more than about a pound every few days.
Parasites, Especially Small Strongyles
Small strongyles (cyathostomes) are the most common internal parasite in adult horses and a frequent cause of persistent loose manure. After a horse ingests larvae while grazing, the larvae burrow into the wall of the large intestine and can lie dormant for months. When they emerge in large numbers, typically in late winter or early spring, they damage the intestinal lining on their way out. This mass emergence, called larval cyathostominosis, causes diarrhea, weight loss, fever, and a dull coat. Even lower-level infections can produce chronically soft manure without obvious illness.
A fecal egg count gives you a baseline, but it won’t detect encysted larvae that haven’t started producing eggs yet. If your horse has persistent loose manure and hasn’t been on a strategic deworming program, parasites should be high on the list of suspects.
Bacterial and Viral Infections
Acute, watery diarrhea that comes on suddenly points toward an infectious cause. The three most common bacterial culprits are Salmonella, Clostridium difficile, and Clostridium perfringens.
- Salmonella typically produces large-volume, watery diarrhea and can progress to bloodstream infection. Affected horses often have a dramatically low white blood cell count.
- C. difficile ranges from explosive, rapidly worsening colitis to a milder, drawn-out course. Horses often develop a fever and go off feed before the diarrhea starts.
- C. perfringens can cause profuse, sometimes bloody diarrhea along with signs of colic and dehydration. It’s tricky to diagnose because healthy horses can shed this bacterium in their manure.
Any of these infections can become life-threatening. A horse with sudden watery diarrhea, especially combined with fever (above 101.5°F), a heart rate over 44 beats per minute, or pale or dark red gums, needs veterinary attention quickly. Capillary refill time, checked by pressing a finger against the gum and watching the color return, should be under two seconds. Anything slower suggests dehydration or compromised circulation.
Antibiotics and Other Medications
Antibiotic-associated diarrhea is the most common drug side effect in horses receiving antimicrobials. These drugs don’t just target the infection; they also wipe out beneficial gut bacteria. Research comparing several common equine antibiotics found that erythromycin (a macrolide) caused the most dramatic disruption to the hindgut microbiome, significantly reducing the fiber-digesting and gut-protective bacteria within one to two days. Doxycycline and metronidazole caused moderate disruption, while trimethoprim-sulfa combinations left the microbial community closest to its original state.
In some regions, veterinarians avoid prescribing macrolides to adult horses altogether because of the diarrhea risk. If your horse develops loose manure while on antibiotics, let your vet know. They may adjust the medication or add a probiotic, though the gut flora can take weeks to fully recover after a course ends.
Sand Accumulation
Horses that eat off sandy ground or graze on sparse, sandy pastures swallow sand with every mouthful. Over time, that sand collects in the large colon, where it acts like fine sandpaper against the intestinal wall. The irritation causes chronic loose manure, weight loss, or intermittent colic. You can check for sand at home by placing a few fecal balls in a rectal glove or ziplock bag, filling it with water, mixing thoroughly, and letting it settle. Sand will collect at the bottom.
Prevention is straightforward: feed hay off rubber mats or in feeders rather than directly on the ground. Psyllium husk supplements, typically given in week-long courses, can help move accumulated sand through the gut, though horses with large accumulations may need veterinary intervention.
Stress and Transportation
Many horse owners notice loose manure during trailering, at competitions, or after changes in routine. This isn’t just anecdotal. Research measuring cortisol (the primary stress hormone) in horses after road transport found that cortisol levels rose significantly and were inversely linked to intestinal motility: the higher the cortisol, the more gut movement slowed. This disruption in normal motility alters how water and nutrients are absorbed across the intestinal wall, producing softer stools. Hot ambient temperatures during transport made the effect worse.
Stress-related loose manure is usually self-limiting. Once the horse returns to a familiar environment and routine, the gut normalizes within a day or two. Frequent travelers who consistently develop loose manure during transport may benefit from slower introductions to travel and adequate hydration before loading.
Free Fecal Water Syndrome
Some horses pass normal, well-formed manure but also expel thin, brownish water before, during, or after defecation. This is free fecal water syndrome, and it’s distinct from true diarrhea. The fecal balls themselves look fine; it’s the liquid running down the hind legs that owners notice, often staining the tail and causing skin irritation.
The condition is not fully understood, but a study in Germany found a surprising pattern: horses lower in the social hierarchy within a group were more likely to develop it, particularly during winter when confined spaces increase social tension. The study found that dental disease, parasites, and cold water intake were not significantly related. Feeding haylage or alfalfa hay has also been associated with the condition in some horses, though responses are highly individual. There are no proven treatments, but some owners find improvement by changing the forage type or adjusting herd dynamics.
Sorting Mild From Serious
A horse that produces cow-patty manure for a day after a feed change or a stressful trailer ride is rarely in danger. The situation shifts when diarrhea is watery, persistent beyond 24 hours, or accompanied by other signs of illness. Normal resting heart rate for an adult horse is 28 to 44 beats per minute, and temperature should fall between 99 and 101.5°F. A horse with diarrhea whose heart rate is elevated, whose gums are pale or dark red, or whose capillary refill is sluggish is showing signs of dehydration or endotoxemia that require veterinary evaluation.
Keeping a mental checklist helps narrow the cause. Ask what changed in the past 48 hours: new hay, new pasture, a grain increase, a deworming, an antibiotic, a trailer ride, a change in herd mates. If nothing changed and the loose manure persists, a fecal egg count and a sand test are inexpensive first steps before moving to more involved diagnostics.