Chronic Diarrhea in Horses: Causes, Diagnosis and Treatment

By Dr Duncan Houston

Chronic diarrhea in a horse is frustrating because it often looks simple from the outside: loose manure, a dirty tail, wet hind legs and a horse that may still seem bright and hungry.

But persistent loose manure is not something to shrug off. Adult horses can lose large amounts of fluid and electrolytes through diarrhea, and chronic cases can point to gut inflammation, sand accumulation, parasites, infection, inflammatory bowel disease, lymphoma, dietary problems or disruption of the normal hindgut microbiome. Diarrhea that persists longer than one month is generally considered chronic, but any adult horse with diarrhea lasting more than a day or two, or recurring repeatedly, deserves veterinary attention. (Merck Veterinary Manual)

The key is to separate three things: true diarrhea, soft manure and free fecal water. They look similar in the stable aisle, but they can mean different things.

Quick Answer

Chronic diarrhea in horses means loose, watery or poorly formed manure that persists or keeps recurring over time. Common causes include diet changes, sand enteropathy, parasites, chronic salmonellosis, inflammatory bowel disease, intestinal lymphoma, malabsorption, dental disease and gut dysbiosis. Because many cases are difficult to diagnose, the safest approach is a structured veterinary workup rather than repeated feed changes, random supplements or blind deworming. (Merck Veterinary Manual)

Is It True Diarrhea or Free Fecal Water?

This distinction matters.

True diarrhea means the manure itself is loose, watery or unformed. It may be cowpat-like, soup-like, explosive or completely watery.

Soft manure means the feces are looser than normal but still partly formed.

Free fecal water means the horse passes formed manure balls but also releases separate liquid before, after or with the manure. Owners often describe this as “water running down the legs” even though the manure balls may look fairly normal.

Free fecal water can still be messy and frustrating, but it is not always the same disease process as true diarrhea. In fact, fecal microbiota transplantation studies in horses suggest that free fecal water does not always behave like classic diarrhea and may not respond to the same gut microbiome approaches. (MDPI)

A useful first step is to take photos or videos of the manure over several days. This helps your vet understand whether the problem is watery diarrhea, loose feces, or formed feces plus separate water.

Why Chronic Diarrhea Is Hard To Diagnose

Chronic diarrhea in horses is difficult because the large colon and cecum are huge fermentation chambers. Many different problems can disrupt water absorption, fermentation, motility, gut bacteria or intestinal lining function.

Merck Veterinary Manual notes that a definitive cause of diarrhea is found in fewer than 50 percent of cases, and chronic diarrhea can be due to inflammatory disease, neoplasia, altered fermentation, dysbiosis, diet change, sand enteropathy, inflammatory bowel disease, intestinal lymphosarcoma, chronic liver disease, abdominal abscesses and other causes. (Merck Veterinary Manual)

That is why the “one magic fix” approach rarely works. Chronic diarrhea usually needs pattern recognition, testing and stepwise management.

Common Causes of Chronic Diarrhea in Horses

University of Melbourne equine guidelines list sand enteropathy, diet, dental disease, parasitism, chronic salmonellosis, alimentary lymphoma and inflammatory bowel disease as causes of chronic diarrhea, while noting that many cases have no identifiable cause and may be associated with gastrointestinal dysbiosis. (Faculty of Science)

How Serious Is Chronic Diarrhea?

Chronic diarrhea ranges from mildly messy to life-threatening.

The clinical checkpoint is this: a bright horse with slightly soft manure is different from a horse with watery diarrhea, fever, colic, dehydration or weight loss.

When Is This an Emergency?

Call your vet urgently if your horse has:

• Profuse watery diarrhea

• Diarrhea with fever

• Colic or repeated pawing, lying down or flank watching

• Depression or weakness

• Dry or tacky gums

• Sunken eyes

• Reduced urination

• Blood or large amounts of mucus in the manure

• Rapid weight loss

• Refusal to eat

• Signs of laminitis, such as reluctance to move, shifting weight or heat in the feet

• Diarrhea after antibiotics, NSAIDs or recent hospitalization

• More than one horse on the property affected

• Any foal with diarrhea

Adult horses can lose massive amounts of fluid rapidly because of the size of the colon and cecum, making diarrhea potentially more dangerous in horses than many owners expect. Merck also advises contacting a veterinarian for diarrhea lasting more than a day or two, or recurring repeatedly. (Merck Veterinary Manual)

If multiple horses are affected, or a horse has acute gastrointestinal signs plus fever, biosecurity matters. AAEP infectious diarrhea guidance recommends isolation or quarantine in scenarios suggesting infectious disease because agents such as equine coronavirus, rotavirus, Salmonella and Clostridioides difficile may have contagious or zoonotic implications.

What Should You Do Right Now?

1. Check the horse, not just the manure

Look at the whole horse.

Check:

• Appetite

• Attitude

• Water intake

• Gum moisture

• Rectal temperature if safe

• Signs of colic

• Weight and body condition

• Digital pulses and hoof heat

• Whether any other horses are affected

If the horse seems dull, painful, febrile, weak or dehydrated, call your vet immediately.

2. Collect a fresh manure sample

A fresh fecal sample can be useful for fecal egg count, sand testing, bacterial culture or PCR panels.

Use a clean container or bag and label it with the horse’s name, date and time. If infectious diarrhea is possible, wear gloves and avoid contaminating shared areas.

3. Keep the horse hydrated

Do not restrict water. Horses with diarrhea need clean water available at all times.

If the horse is not drinking, is dehydrated or has watery diarrhea, veterinary fluid therapy may be needed. Severe ongoing fluid and electrolyte losses may require intravenous fluids. (Merck Veterinary Manual)

4. Avoid sudden feed changes

Do not panic-change everything at once.

Keep the diet simple and consistent while you speak with your vet. Sudden changes in hay, pasture, grain, supplements and oils can make it harder to know what helped or worsened the problem.

5. Do not start antibiotics without advice

Antibiotics are not automatically helpful for chronic diarrhea. In some cases, they can worsen dysbiosis and delay recovery. University of Melbourne guidelines specifically note that antimicrobial therapy is not indicated for chronic diarrhea in general and may delay recovery because of ongoing dysbiosis. (Faculty of Science)

6. Do not deworm blindly

Parasites can cause chronic diarrhea, especially cyathostomins, but treatment should be planned carefully. Fecal egg counts are useful, but a negative fecal egg count does not rule out cyathostomin disease because larval stages may not be shedding eggs. (Faculty of Science)

This is where vet-directed parasite control beats stable-yard guesswork.

How Vets Diagnose Chronic Diarrhea

A good workup starts with the history.

Your vet will want to know:

• How long the diarrhea has been happening

• Whether it is constant or intermittent

• Whether manure is watery, soft or free fecal water

• Recent feed, hay, pasture or supplement changes

• Recent antibiotics, NSAIDs or deworming

• Travel, showing, hospitalization or stress

• Parasite control history

• Dental history

• Weight changes

• Appetite and water intake

• Whether other horses are affected

• Any fever, colic, laminitis or lethargy

Diagnostic tests may include:

• Physical examination

• Rectal temperature and hydration assessment

• Complete blood count

• Serum biochemistry

• Electrolytes

• Kidney and liver values

• Albumin and total protein

• Inflammatory markers such as fibrinogen or serum amyloid A

• Fecal egg count

• Fecal PCR or culture for pathogens such as Salmonella

• Sand sedimentation test

• Abdominal radiographs for sand

• Abdominal ultrasound

• Rectal examination

• Rectal biopsy

• Glucose absorption test

• Abdominocentesis in selected cases

• Intestinal biopsy via laparoscopy or surgery in difficult cases

University of Melbourne guidelines highlight the importance of assessing dehydration, electrolyte abnormalities and renal function, and note that fecal PCR or culture may be needed to rule out salmonellosis, serial samples may be required, and definitive diagnosis of inflammatory bowel disease or lymphoma may require histopathology of intestinal tissue. (Faculty of Science)

Important Rule-Outs Your Vet May Consider

Sand enteropathy

Sand can irritate the colon and cause diarrhea, recurrent colic or weight loss. It is more likely in horses kept on sandy soil, fed hay or grain directly on sandy ground, or grazing sparse sandy paddocks. Sand may be detected by fecal sedimentation, abdominal radiographs or ultrasound depending on the case. (Faculty of Science)

Cyathostomins

Small strongyle larvae can cause serious colitis and diarrhea. Fecal egg counts help with parasite assessment, but they do not always rule out larval cyathostomin disease. Treatment should be vet-directed because parasite die-off can worsen inflammation in some affected horses. (Faculty of Science)

Salmonella and infectious diarrhea

Salmonella can cause anything from carrier status to severe watery diarrhea, fever, dehydration and septicemia. Some horses can shed Salmonella for prolonged periods, especially after stress, illness, transport or hospitalization. (Merck Veterinary Manual)

Inflammatory bowel disease

Inflammatory bowel disease is a group of disorders involving inflammatory cell infiltration of the intestinal lining. Horses may show chronic diarrhea, weight loss, poor condition, low protein or malabsorption. Definitive diagnosis may require tissue biopsy. (Faculty of Science)

Intestinal lymphoma

Alimentary lymphoma is uncommon but important. It can disrupt intestinal function and is often associated with weight loss and protein loss. Prognosis is generally poor compared with more manageable causes such as diet or sand. (Faculty of Science)

Dysbiosis

Dysbiosis means disruption of the normal gut microbial population. It may follow antibiotics, illness, diet changes, stress or other intestinal disease. Chronic diarrhea can take time to improve because the hindgut flora may need time to normalize. (Faculty of Science)

Right dorsal colitis and NSAID injury

Horses treated with nonsteroidal anti-inflammatory drugs, especially if high doses or prolonged courses are involved, can develop colonic injury. AAEP lists right dorsal colitis associated with NSAID administration as an important non-infectious differential for adult horses with diarrhea.

Treatment Depends on the Cause

There is no single treatment for chronic diarrhea in horses.

A treatment plan may include:

Supportive care

Horses with dehydration, electrolyte loss, fever, colic or systemic illness may need fluids, electrolyte correction, anti-inflammatory treatment, endotoxin support and close monitoring. Severe acute worsening should not be managed with supplements alone. (Merck Veterinary Manual)

Diet stabilization

Many chronic cases benefit from a simple, consistent diet while the workup is underway.

This may include:

• High-quality forage

• Gradual feed transitions

• Reducing sudden pasture changes

• Reviewing alfalfa, grain, oil and supplement intake

• Avoiding high-starch overload

• Checking dental function

• Ensuring clean water access

Soft manure after lush pasture, alfalfa hay, transport, racing, showing or temporary stress may occur in otherwise healthy horses, but persistent or recurrent diarrhea should still be assessed to rule out infectious or medical causes. (Merck Veterinary Manual)

Sand management

If sand is involved, treatment may include removing sand exposure and using vet-directed therapy. University of Melbourne guidelines note that published research collectively supports combination therapy for sand enteropathy under veterinary administration, while also noting that feeding psyllium as prevention has no advantage over simply removing access to sand. (Faculty of Science)

In plain English: do not keep feeding a horse on sand and expect a supplement to fix the problem.

Parasite treatment

If cyathostomins or other parasites are suspected, your vet may recommend a specific deworming protocol and, in some clinically affected horses, anti-inflammatory support around treatment. Do not assume a single dewormer dose is the answer for every chronic diarrhea case. (Faculty of Science)

Treatment for inflammatory bowel disease

Inflammatory bowel disease is often treated with corticosteroids or other immune-modifying medication under veterinary supervision. Prognosis is guarded, and some horses require long courses and careful monitoring. (Faculty of Science)

Fecal microbiota transplantation

Fecal microbiota transplantation, or FMT, involves transferring fecal material from a healthy donor horse to a recipient to help restore a healthier gut microbial community. A 2023 systematic review found FMT to be promising for some equine gastrointestinal disorders, including colitis and diarrhea, but emphasized that evidence quality is limited by small sample sizes, lack of control groups and uncertainty around donor selection, dosing and long-term safety. (MDPI)

FMT is not a DIY manure smoothie project. Donor screening, case selection and veterinary supervision matter.

Probiotics and prebiotics

Some horses improve with carefully chosen digestive support, but probiotics are not a guaranteed fix. Evidence in horses is mixed, and some studies in foals have even shown worse outcomes with certain probiotic use.

If a product helps a particular horse, fine. But if chronic diarrhea is persistent, worsening or associated with weight loss, a supplement should not replace diagnostics.

What Not To Do

Do not ignore chronic loose manure because the horse seems bright

Some horses with chronic diarrhea look deceptively well until weight loss, dehydration, low protein or laminitis risk becomes obvious.

Do not keep changing feeds every few days

Rapid diet changes can worsen hindgut instability and make it impossible to know what is helping.

Do not give leftover antibiotics

Antibiotics can worsen dysbiosis and may be inappropriate unless a specific indication exists.

Do not rely only on probiotics

They may help some horses, but they do not rule out sand, parasites, infection, IBD or lymphoma.

Do not deworm repeatedly without a plan

Parasites matter, but blind repeated deworming can miss the diagnosis and may not be safe in every case.

Do not forget biosecurity

If diarrhea is sudden, watery, febrile or affecting more than one horse, isolate the horse and use hygiene precautions until your vet advises otherwise. AAEP guidance highlights that some infectious causes of equine diarrhea have herd health or zoonotic implications.

How To Prevent Chronic Diarrhea Problems

Not every case can be prevented, but good management reduces risk.

Helpful steps include:

• Make feed changes gradually

• Keep forage consistent where possible

• Avoid sudden lush pasture exposure

• Feed off mats, tubs or feeders in sandy areas

• Improve footing around hay and feeding zones

• Maintain a vet-directed parasite control program

• Do fecal egg counts as advised

• Keep dental care up to date

• Use NSAIDs only as directed

• Avoid unnecessary antibiotics

• Provide clean water at all times

• Reduce stress during travel, showing and herd changes

• Quarantine new arrivals when appropriate

• Keep manure logs for horses with recurrent loose feces

• Investigate recurring diarrhea early rather than waiting months

The best prevention is not dramatic. It is steady feeding, parasite control, dental care, clean water and early attention when manure changes persist.

Will My Horse Be Okay?

Many horses with chronic diarrhea improve once the underlying trigger is identified and managed. Diet-related cases, sand-associated cases and some parasite-related cases may respond well when the plan is correct.

Other causes are harder. Inflammatory bowel disease has a guarded prognosis, and intestinal lymphoma carries a poor prognosis. Even when the primary cause is treated, diarrhea may take time to resolve because the gut flora and intestinal lining need time to stabilize. University of Melbourne guidelines note that normalization of gut flora can take time, and prognosis depends heavily on the underlying diagnosis. (Faculty of Science)

The main thing is not to guess for months. The sooner the workup begins, the better the chance of finding a manageable cause.

FAQs

What counts as chronic diarrhea in horses?

Diarrhea that persists longer than one month is generally considered chronic. However, any adult horse with diarrhea lasting more than a day or two, or recurring repeatedly, should be discussed with a vet. (Merck Veterinary Manual)

Can chronic diarrhea be caused by feed?

Yes. Feed changes, lush pasture, alfalfa, high-starch diets, sudden supplement changes and altered hindgut fermentation can all contribute. Feed may not be the only cause, so persistent diarrhea still needs assessment.

Is chronic diarrhea contagious?

Sometimes. Causes such as Salmonella, Clostridioides difficile, equine coronavirus and rotavirus can have biosecurity implications. If diarrhea is acute, watery, febrile or affecting multiple horses, isolate the horse and call your vet.

Are probiotics good for chronic diarrhea in horses?

They may help selected horses, but evidence is mixed. They should not replace a workup for sand, parasites, infection, inflammatory bowel disease or lymphoma.

When should I call a vet?

Call a vet if diarrhea lasts more than a day or two, keeps recurring, becomes watery, or is associated with fever, colic, weight loss, dehydration, blood, mucus, reduced appetite or depression. Call urgently for any foal with diarrhea.

Final Thoughts

Chronic diarrhea in horses is not just a stable-cleaning problem.

It is a sign that the gut is not handling water, fermentation, inflammation or absorption normally. Sometimes the cause is manageable, such as diet, sand or parasites. Sometimes it is more serious, such as inflammatory bowel disease, chronic infection or lymphoma.

The safest approach is structured: define the manure pattern, check the whole horse, collect a fecal sample, avoid random treatment, review diet and parasite history, and involve your vet early. Chronic diarrhea often takes patience, but a clear plan is far better than months of trial and error.

If the horse is bright and stable, you have time to investigate properly. If the horse is watery, weak, febrile, colicky, dehydrated or losing weight, do not wait.

If you are unsure whether your horse’s diarrhea is mild, chronic, infectious, diet-related or urgent, ASK A VET™ can help you work through the signs and decide what to do next.