Horse manure and digestive changes: A guide to understanding what you see

The Microbiome Management seriesPillar 4 of 6

Something is different in the stall this morning. Liquid down a hind leg, a pile that has lost its shape or manure that is plainly loose. The first instinct is to name it, and a search will offer a name within seconds. The more useful first question is what changed.

Manure is the last page of a long story. By the time a pile lands in the bedding, the hay has been chewed, digested, fermented by the microbes in the hindgut, and relieved of water in the colon until it holds its shape. When the shape changes or the water arrives separately, something upstream changed with it: what he ate, how much he drank, how fast things moved, what the microbes were doing with the fiber. This guide helps you read what you are seeing, and know the few signs that mean picking up the phone today.

Why manure changes

A horse cannot digest fiber on his own. The microbes in his cecum and large colon do it, fermenting hay and grass into the fatty acids he runs on.¹ Further along, the colon recovers water, and the small colon forms the fecal balls you pick out each morning.²

So a pile reflects three things at once: what reached the microbes, how they worked on it, and how much water came back out of it on the way. Change any one and the pile can change.

What a pile reflects

What reached the microbes

The hay, the grass, the feed, and how quickly any of them changed.

How they worked on it

Fermentation in the cecum and large colon, by a community that follows the diet.

How much water came back

Drinking, and the water the colon recovers before the balls form.

The community moves faster than most owners expect. When ponies were switched abruptly between grass and hay, their gut community shifted within the first few days of each change.³ Yearlings moved onto pasture had manure bacteria resembling the pasture horses’ within four days.⁴ A new load of hay, a week of spring grass, a weekend of drinking less at a show: from the microbes’ side, each one is a change in conditions.

That is why the first useful question is not “what is wrong with him” but “what changed”.

Three things you might be seeing

“Loose”, “wet” and “scouring” mean different things to different people. A short description travels further than a label, and it is what lets you compare this week with last.

Look at fresh manure where you can. Rain, bedding, trampling and time on the ground all change how a pile looks. If several horses share the space, be honest about whether you saw this horse pass it or are assuming.

What a label leaves out

“Wet”

Is the liquid passing separately from formed balls, or is the manure itself watery?

“Loose”

How far from this horse’s usual, and in how many piles?

“Scouring”

Since when, and is the horse passing more often or in greater volume than usual?

Formed manure with separate fecal water

Some horses pass recognizable fecal balls and a separate liquid, before, during or after the solid material. Researchers call this free fecal liquid or free fecal water. Fecal water syndrome is the term most owners use.⁵

The solid part has formed, and the liquid is passing separately. Why that happens is still being worked out, and the hindgut is where researchers are looking.^5,6

“He passed formed balls, then brown liquid ran down his hind legs” says far more than “his manure was wet”. If the skin under the tail is soiled or sore, note that too.

For the focused explanation, read Fecal water in horses: What the research found and where to start.

Softer or less-formed manure

“Softer manure” describes something you saw, not a disease. Fecal balls that flatten more readily, a pile with less shape or piles that vary from one to the next.

Say how far it has moved from usual and how often you have seen it. “Three piles were softer than usual this morning” is useful. “His digestion is bad” is not.

Loose manure in horses: What to notice and what to discuss with your veterinarian takes this further.

Diarrhea

Diarrhea means the manure itself is abnormally loose or watery: more water than usual is reaching the end of the tract. Note whether it has lost its form, and whether the horse is passing it more often or in greater volume than usual. New diarrhea is one of the signs in the last section that call for your veterinarian the same day.

Fecal water or diarrhea? Understanding the difference in horses explains the terms. Diarrhea in horses: Why veterinary assessment matters and what to report covers assessment and what to say.

Read the horse alongside the pile

A pile is one observation. A few others belong beside it, because they change what it means.

Is he eating, and finishing? Is he bright and interested, or quiet? Is he drinking as usual, as far as you can see? A comfortable, hungry horse with softer manure is a different morning from a quiet one leaving his hay.

Teeth come first in the digestive chain. Dropping partly chewed feed, called quidding, or reluctance to chew hay points toward a dental check.⁷ Teeth wear and change with age, which is one reason routine dental exams matter more as a horse gets older.⁸

Note weight or condition alongside manure, even when manure is what caught your eye. Poor weight gain in horses: Where digestion fits in the bigger picture takes the wider view.

Then the calendar. A new hay batch, a move onto grass, travel, deworming or medication, and new arrivals at the barn all belong beside the description. A recent event is often the most useful clue you have. For how to keep that record against your own horse’s normal, read Digestive Stability in horses: How to tell whether a change holds.

When it keeps coming back

A pattern of improvement and relapse wears everyone down, and it tempts everyone involved to start again each time with a different feed or supplement.

Bring the episodes together in one account, with dates, what the horse was eating, what else was going on and which professional assessments happened. Include the ordinary stretches, not only the memorable bad days. Leave a gap as a gap.

One account, across episodes

1. Mar 3 to 9Fecal water after formed balls, most mornings. New hay batch from Mar 1. Veterinary visit Mar 6.
2. Mar 10 to Apr 21Usual pattern. Same hay, same turnout.
3. Apr 22 to 27Not recorded. Owner away, barn staff feeding.
4. Apr 28 to May 5Fecal water again, two or three mornings a week. Same hay. Dewormed Apr 25. Call booked May 2.

If this sounds familiar, you are not alone. It improves. Something changes. Then it comes back. When a pattern keeps returning, the calendar beside it is often where the next clue is. Digestive Stability in horses: How to tell whether a change holds shows how to judge whether the next improvement is the one that stays, and Why do my horse’s digestive changes keep coming back? addresses recurrence directly.

What the research says about fecal water

Two recent studies compared the gut bacteria of horses with fecal water against healthy horses from the same barns. The larger, in Missouri, found the communities differed.⁶ The smaller, in Canada, did not find a significant difference.⁵

Canada, 2024

No significant difference

14 horses with fecal water, 11 healthy stablemates. Fecal bacteria sequenced and compared.⁵

Missouri, 2025

Some differences

32 horses with fecal water, 51 healthy horses from the same barns. Differences in the bacterial community between the groups.⁶

The research is young. What is well established is that the hindgut community follows what the horse eats, often within days.^3,4 That makes the conditions you set worth managing, whatever any one organism turns out to mean.

Managing the conditions

Managing those conditions is the idea behind the Microbiome Management Framework. Rather than chase one missing organism, it starts with the environment the whole community lives in: forage, water, routine, transitions and careful observation, with Digestive Stability as the goal. Its first stage is that environment itself. Microbiome Management for horses: A framework for Digestive Stability sets it out, and Supporting your horse’s gut health through daily management puts it into the barn day.

Where Humequine fits

We make Humequine for owners who manage the hindgut as a daily routine, the same way they manage the hay and the water. Humequine is Microbiome Management for Horses: it supports the environment that beneficial bacteria need, so the community already living in your horse can grow and stabilize. It works at the first stage of the Microbiome Management Framework, the environment itself. Where Humequine fits within a Microbiome Management program covers the bottle, the measure and the morning feed.

Signs that mean a call to your veterinarian today

Most changes in manure are worth noting and watching against your horse’s normal. A few are worth a call the same day.

New diarrhea is one of them, and it is worth a call right away if it is profuse or watery, if he is going downhill quickly, or if pain, fever, weakness or dullness comes with it. A horse can lose a lot of fluid in a short time, and diarrhea in an adult horse has many possible causes, which is why the history and an examination matter.^9,10

Signs of abdominal pain are another: pawing, looking at the flank, kicking at the belly, rolling, restlessness, sweating, eating less or unusual dullness. Colic has many causes, and you do not need the full list of signs before you call. Give no medication unless your veterinarian tells you to.¹¹

Fecal water that persists, softer manure that keeps coming back, or loss of condition are worth raising at the next conversation, even in a comfortable horse.

When you call, the description you have built is exactly what helps.

1. The horseAge, relevant diagnoses and usual routine.
2. The observationWhat changed, when you first noticed it and whether you saw it passed.
3. Associated signsAppetite, behavior, any apparent change in drinking and condition.
4. Recent historyForage or feed changes, travel, new arrivals, medication, deworming and any other sick horses.
5. Anything already givenThe exact product or medicine, the amount if you know it and the time.

Bring the packaging, or a photograph of the label, for anything you have given. Ask before you collect a fecal sample, since different tests need different handling.

Some causes of diarrhea can spread between horses, and some to people. Until your veterinarian says otherwise, tell barn management, give the horse its own equipment, handle it last and wash your hands afterward.^10,12 If he needs to travel to a clinic, call ahead so staff can plan the arrival.

A note on foals: this guide is written for adult horses. For a foal, your veterinarian is the right first call about any change in manure.

Frequently asked questions

Why has my horse’s manure changed?

Manure is the end of a long process: the microbes in the hindgut ferment the fiber, and the colon recovers water and forms the fecal balls. A change in what he eats, how much he drinks, how fast things move or what the microbes are doing can all change the pile. The hindgut community can shift within days of a feed change, so the calendar is often the first clue.

What is fecal water in horses?

Some horses pass recognizable fecal balls and a separate liquid, before, during or after the solid material. Researchers call this free fecal liquid or free fecal water, and fecal water syndrome is the term most owners use.

What is the difference between fecal water and diarrhea in horses?

With fecal water, the manure is formed and a liquid passes separately. With diarrhea, the manure itself is abnormally loose or watery. Telling the two apart makes your description far more useful.

Can a new load of hay change my horse’s manure?

It can. The microbes in the hindgut respond to what reaches them. In one study, ponies switched abruptly between grass and hay showed shifts in their gut community within the first few days of each change. A new batch of hay is a smaller change of the same kind, which is why it is worth introducing gradually.

What does research say about fecal water and the microbiome?

Two recent studies compared the gut bacteria of horses with fecal water against healthy horses from the same barns. The larger, in Missouri, found the communities differed. The smaller, in Canada, did not find a significant difference. Both were observational, so neither shows cause, and the research is still young.

When should I call the vet about my horse’s diarrhea?

Call promptly about any new diarrhea, and right away if it is profuse or watery, if the horse is going downhill quickly, or if pain, fever, weakness or dullness comes with it. A horse can lose a lot of fluid in a short time.

Can horse diarrhea spread to other horses or people?

Some causes can. Until your veterinarian says otherwise, tell barn management, give the horse its own equipment, handle it last and wash your hands afterward.

References

1. University of Maryland Extension. Teaching Basic Equine Nutrition Part II: Equine Digestive Anatomy and Physiology. extension.umd.edu/resource/teaching-basic-equine-nutrition-part-ii-equine-digestive-anatomy-and-physiology
2. Iowa State University Extension and Outreach. Synopsis of the Digestive Anatomy and Physiology of the Horse. www.extension.iastate.edu/equine/synopsis-digestive-anatomy-and-physiology-horse
3. Garber A, Hastie P, McGuinness D, Malarange P, Murray JA. Abrupt dietary changes between grass and hay alter faecal microbiota of ponies. PLOS ONE. 2020;15(8):e0237869. doi.org/10.1371/journal.pone.0237869
4. Fernandes KA, Kittelmann S, Rogers CW, and colleagues. Faecal Microbiota of Forage-Fed Horses in New Zealand and the Population Dynamics of Microbial Communities following Dietary Change. PLOS ONE. 2014;9(11):e112846. doi.org/10.1371/journal.pone.0112846
5. Wester RJ, Baillie LL, McCarthy GC, Keever CC, Jeffery LE, Adams PJ. Dysbiosis not observed in Canadian horses with free fecal liquid (FFL) using 16S rRNA sequencing. Scientific Reports. 2024;14:12903. doi.org/10.1038/s41598-024-63868-1
6. Porter MM, Davis DJ, McAdams ZL, Townsend KS, Martin LM, Wilhite C, Johnson PJ, Ericsson AC. Alterations in the Microbiome of Horses Affected with Fecal Water Syndrome. Veterinary Sciences. 2025;12(8):724. doi.org/10.3390/vetsci12080724
7. University of Minnesota Extension. Caring for your horse’s teeth. extension.umn.edu/agriculture/animals-and-livestock/horse/caring-for-your-horses-teeth
8. University of Minnesota Extension. Caring for your senior horse. extension.umn.edu/agriculture/animals-and-livestock/horse/caring-for-your-senior-horse
9. Stewart AJ. Overview of Infectious Diarrheal Diseases in Horses. Merck Veterinary Manual. Reviewed October 2022, modified July 2026. www.merckvetmanual.com/digestive-system/infectious-diarrheal-diseases-in-horses/overview-of-infectious-diarrheal-diseases-in-horses
10. American Association of Equine Practitioners, Field Guidelines Subcommittee. Acute Infectious Diarrhea Field Diagnostic Guidelines. 2025. aaep.org/resource/equine-acute-infectious-diarrhea-field-diagnostic-guidelines/
11. Young A. Colic Happens: What You Can Do Before, During, and After a Colic. UC Davis Center for Equine Health, Horse Report. 2024. cehhorsereport.vetmed.ucdavis.edu/news/colic-happens
12. UC Davis Center for Equine Health. Diseases with horse to human transmission. ceh.vetmed.ucdavis.edu/diseases-horse-human-transmission

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