Why Does My Dog Keep Having Diarrhea? Causes, Gut Testing & What to Do Next

Written by Dr. Katie Woodley, Holistic Veterinarian and Founder of The Natural Pet Doctor

If your dog keeps having diarrhea that improves and then comes back again, there's an important question to ask:

Recurring diarrhea in dogs can be associated with intestinal parasites such as Giardia, changes in the gut microbiome, food-responsive disease, digestive dysfunction, chronic enteropathy, intestinal inflammation, stress, and other gastrointestinal or systemic conditions.

And if your dog is also experiencing mucus or blood in the stool, vomiting, appetite changes, or weight loss, I don't want to simply keep reaching for another probiotic or changing foods without understanding why these symptoms are happening.

As a holistic veterinarian who has spent years working with dogs and cats with chronic gut problems, my approach is to gather information first and then use that information to determine what the individual pet's gastrointestinal tract actually needs.

Why Does My Dog Keep Getting Diarrhea?

Recurring diarrhea in dogs means we need to look beyond the individual episode and investigate what may be repeatedly irritating, disrupting, or inflaming the gastrointestinal tract.

Possible causes of recurring diarrhea in dogs include:

• Intestinal parasites, including Giardia
• Dysbiosis or disruption of the gut microbiome
• Food-responsive enteropathy
• Chronic inflammatory enteropathy
• Inflammatory bowel disease (IBD)
• Digestive or pancreatic dysfunction
• Intestinal barrier dysfunction
• Medication-associated changes within the gastrointestinal tract
• Stress and gut-brain axis dysfunction
• Other gastrointestinal or systemic diseases

One episode after your dog eats something unusual is very different from a dog who has diarrhea every few weeks for six months.

That's why one of the first things I teach pet parents is to stop looking at every flare as a completely separate event.

If your dog gets better and then repeatedly relapses, we need to start asking what those episodes have in common.

Can Environmental Allergies Cause Diarrhea and Vomiting in Dogs?

Environmental allergies and gastrointestinal problems can certainly coexist in the same dog. The skin, immune system, microbiome, and gastrointestinal tract don't operate independently from one another.

However, recurrent vomiting, diarrhea, mucus, or blood in the stool warrants investigation of the gastrointestinal tract itself rather than automatically assuming environmental allergies explain all of the symptoms.

When I see that combination, I start asking:

• Have parasites been appropriately ruled out?
• Could dysbiosis be contributing?
• Is there intestinal inflammation?
• Is digestion working appropriately?
• Is the intestinal barrier compromised?
• Could food be contributing?
• Do we need to investigate chronic enteropathy or IBD?

This is where I want to move from guessing to gathering information.

Step 1: Rule Out Parasites — Including Giardia

One of the first things I want to know with recurring diarrhea is:

A previous negative fecal test doesn't necessarily mean every potential parasite has been excluded.

Different testing methods provide different information, and your veterinarian can determine which tests are appropriate based on your dog's symptoms, history, and exposure risks.

Can Giardia Cause Recurring Diarrhea in Dogs?

Yes. Giardia can cause gastrointestinal signs in dogs, including diarrhea, and is one potential cause to consider when GI symptoms keep recurring.

Depending on your dog's situation, your veterinarian may use fecal examination, antigen testing, PCR, or other testing methods.

Instead of only asking:

"Was my dog's fecal test negative?"

Consider asking:

"How was Giardia ruled out?"

This doesn't mean Giardia is behind every case of recurring diarrhea. It means I don't want to spend months changing foods and adding supplements while overlooking a potential underlying contributor.

Step 2: Investigate the Gut Microbiome

Your dog's gastrointestinal tract contains an enormous ecosystem of microorganisms collectively known as the gut microbiome.

These microorganisms interact with digestion, immune function, intestinal health, and the gut-brain axis. When that microbial ecosystem becomes disrupted, we call it dysbiosis.

What Is Dysbiosis in Dogs?

Dysbiosis is an alteration in the intestinal microbial community and can occur alongside gastrointestinal disease. Diet, antibiotics, certain medications, inflammation, illness, and stress may all influence the microbiome.

And here's where I see pet parents get stuck.

Their dog has diarrhea. They try a probiotic. Maybe it helps temporarily. Maybe it makes things worse.

They buy another probiotic. Then they change the food. Then they add digestive enzymes.

Eventually there's an entire cabinet of supplements — but they still don't understand why the diarrhea keeps coming back.

This is one reason I may use microbiome testing in dogs with chronic or recurring GI issues.

Microbiome testing doesn't explain every gastrointestinal problem, but it can provide another piece of information about the intestinal ecosystem rather than continually trying to manipulate that ecosystem without understanding what may be happening.

Step 3: Look Deeper at Gut Function

Routine veterinary diagnostics remain incredibly important.

Depending on your dog's symptoms and history, your veterinarian may recommend bloodwork, fecal testing, imaging, ultrasound, GI-specific blood testing, diet trials, or additional diagnostics.

But sometimes pet parents come to me saying:

Normal routine bloodwork doesn't mean your dog's symptoms aren't real. It may mean we need to investigate a different part of the health picture.

What Is Functional Gut Testing for Dogs?

Functional gut testing evaluates biomarkers associated with different aspects of gastrointestinal function. Depending on the test, these may provide additional information about intestinal inflammation, digestion, immune activity, microbial activity, and intestinal barrier function.

But testing isn't about collecting as much data as possible.

Can Functional Gut Testing Diagnose IBD in Dogs?

No. A functional stool test or microbiome test cannot independently diagnose inflammatory bowel disease or chronic inflammatory enteropathy in a dog.

These tests may provide additional information about gastrointestinal function or inflammation, but diagnosis may require other veterinary diagnostics depending on the individual dog.

That's especially important if your dog is experiencing:

• Weight loss
• Persistent or worsening diarrhea
• Repeated vomiting
• Significant blood in the stool
• Appetite loss
• Abdominal discomfort
• Changes in energy

Think of functional testing as another layer of information, not a replacement for veterinary medicine.

What If My Dog Has Diarrhea AND Vomits Bile?

This is a pattern I pay particular attention to.

When recurring diarrhea occurs alongside bile vomiting, reflux-like symptoms, appetite changes, or weight loss, I become even more interested in what's happening throughout the gastrointestinal tract.

Occasional bile vomiting can happen for different reasons, but recurring bile vomiting shouldn't automatically be dismissed as simply an "empty stomach" problem.

Depending on the individual pet, we may need to think more broadly about upper gastrointestinal function, inflammation, bile flow, diet-responsive disease, chronic enteropathy, and other potential causes.

Which Gut Test Should I Start With?

This is where pet parents understandably get overwhelmed.

Do you need a parasite test? A microbiome test? A comprehensive functional gut test? Bloodwork? An ultrasound?

The appropriate starting point depends on your dog's symptoms, history, previous testing, and — most importantly — what question you're trying to answer.

• Parasite testing asks whether an infectious or parasitic organism could be contributing.
• Microbiome testing evaluates the intestinal microbial ecosystem and dysbiosis patterns.
• Functional gut testing evaluates biomarkers associated with different aspects of gastrointestinal function.
• Bloodwork and imaging evaluate completely different pieces of the health picture.

These tests aren't necessarily competing with one another. They're answering different questions.

Testing Is Only the Beginning

Let's say you've gathered more information.

Now what?

This is where I see another common mistake.

A pet parent receives test results and suddenly introduces a new diet, three herbs, two probiotics, digestive enzymes, a gut powder, an immune supplement, and maybe a detox product.

Then the dog has diarrhea again.

This is why I use a framework.

Especially with sensitive pets, my approach is slow and steady.

Gather information. Prioritize. Introduce changes intentionally. And give the body time to respond.

This is where my 5R Gut Health Framework comes in.

The 5R Gut Health Framework for Dogs

The 5Rs Are NOT Five Supplements

You don't need one product for Remove, another product for Replace, another for Repair, and so on.

The 5Rs are a framework for thinking through the case.

Your dog's symptoms, history, veterinary diagnostics, and additional testing help determine which areas actually need attention.

And equally importantly: what doesn't your dog need right now?

More isn't always better, especially with sensitive pets.

What About Broader Immune and Whole-Body Support?

Gut health doesn't exist in isolation. Depending on the individual pet, I may also think about broader immune and whole-body support after we've addressed the more immediate priorities.

Medicinal mushrooms are one tool I may consider depending on the pet's overall health picture.

Why Might Probiotics Make a Sensitive Dog Worse?

Some dogs with sensitive gastrointestinal tracts may experience increased gas, bloating, or stool changes after introducing a probiotic or microbiome-directed product.

That doesn't necessarily mean:

"My dog can't take probiotics."

It means we may need to consider:

• The product
• The ingredients
• The amount
• The timing
• The underlying intestinal environment
• Whether another problem needs to be addressed first

When Should I Take My Dog to the Veterinarian for Diarrhea?

Most pet parents searching for natural diarrhea remedies also need to know when not to manage diarrhea at home.

Contact your veterinarian promptly if diarrhea is severe, persistent, worsening, or accompanied by concerning symptoms such as:

• Significant or increasing blood
• Black or tarry stool
• Repeated vomiting
• Severe lethargy or weakness
• Abdominal pain or swelling
• Dehydration
• Refusal to eat or drink
• Possible toxin exposure
• Possible foreign-body ingestion
• Collapse or rapidly worsening symptoms

Puppies, senior dogs, extremely small dogs, and pets with underlying medical conditions may require veterinary assessment sooner.

An at-home gut test isn't an emergency test. When in doubt, contact your veterinarian.

Frequently Asked Questions About Recurring Diarrhea in Dogs

Stop Chasing the Diarrhea and Start Investigating the Pattern

If your dog is having diarrhea today, appropriately supporting the immediate flare matters.

But if you've been going through this for months...

The diarrhea gets better and comes back.
There's mucus again.
You occasionally see blood.
Your dog vomits bile.
You've changed foods three times.
There's another probiotic sitting in your cabinet.

I want you to change the question.

Ask:

That's where appropriate veterinary diagnostics, additional testing when indicated, and an intentional framework can help us make more informed decisions about what that individual dog actually needs.

Because stopping the diarrhea and understanding why your dog keeps getting diarrhea are two very different things.

Continue Learning About Your Dog's Gut Health