Diarrhoea: stabilising digestion by identifying and treating root causes

Chronic diarrhoea can leave you feeling drained and unwell. Functional medicine investigates the deeper causes, from gut infections to food sensitivities, to restore digestive balance and long-term health.

middle aged man holding cup of tea smiling looking out window

How to stop diarrhoea – natural diarrhoea relief

Diarrhoea can be uncomfortable and embarrassing. Discover more about chronic diarrhoea treatment to find out how to get lasting diarrhoea relief. This page covers:

At Melbourne Functional Medicine, we provide a natural diarrhoea treatment, working closely with you to identify and treat the root cause of your diarrhoea using our award winning approach to healthcare.

What is diarrhoea?

Understanding your condition

Diarrhoea is defined as an unformed, mushy or watery bowel movement, often with increased frequency and a sense of urgency. Diarrhoea may occur as an isolated acute condition, be ongoing (chronic), or a symptom of another condition. Other symptoms can be present, and these may help identify the underlying cause alongside testing.

middle aged man sitting on toilet with toilet roll gripping fingers tightly around knees
middle aged man sitting on toilet with toilet roll gripping fingers tightly around knees

What is diarrhoea?

Understanding your condition

Diarrhoea is defined as an unformed, mushy or watery bowel movement, often with increased frequency and a sense of urgency. Diarrhoea may occur as an isolated acute condition, be ongoing (chronic), or a symptom of another condition. Other symptoms can be present, and these may help identify the underlying cause alongside testing.

melbourne functional medicine team member holding probiotic supplements reading labels

Providing a diarrhoea natural treatment

Once the cause is identified, natural diarrhoea relief from a functional medicine practitioner can be gentle, safe and effective. Our team of digestive health experts take a holistic, personalised approach to helping people with chronic diarrhoea get well again.

Diarrhoea symptoms

The main symptom of diarrhoea is a watery or mushy stool, identified as types 5, 6 & 7 on the Bristol Stool Scale. Three or more watery or mushy movements within 24 hours would be considered as diarrhoea. The exception, however, is loose stools (non-watery) in exclusively breastfed babies which is considered as normal, however, if there is concern, this should be checked with a practitioner or maternal health nurse.

Dehydration is the most severe threat posed by diarrhoea, where electrolytes (sodium, chloride, bicarbonate, potassium and magnesium) are lost through sweat, urine, vomit, breathing and watery stools, and can be life-threatening if allowed to persist. Dehydration signs in order of severity and usual onset include:

  • Thirsty, drinks eagerly
  • Sunken eyes
  • Irritability, restlessness
  • Loss of skin elasticity (when doing a skin pinch test on the back of the hand, the skin takes more than two seconds to return to normal)
  • Drinks poorly, unable to drink
  • Lethargy
  • Unconsciousness

Diarrhoea can be acute or chronic, with possibly slightly varying symptoms.

 

Acute diarrhoea

Acute diarrhoea is often due to gastroenteritis from a food or water-borne infectious pathogen (parasite, protozoa, virus or bacteria), or from contact with an infected person. If left untreated, it can be life-threatening, and medical attention should be sought if symptoms persist for more than 24 hours.

Infectious diarrhoea is often accompanied by any of the following symptoms:

  • Explosive, frequent, watery stools
  • Fever, chills, sweating
  • Abdominal pain, griping, or cramps
  • Excessive, smelly flatulence
  • Malaise, fatigue
  • Nausea, vomiting
  • Dehydration
  • Skin rash
  • Urgency

 

Chronic diarrhoea

Chronic diarrhoea affects around 5% of people in the Western world. It is more commonly associated with other health conditions that have their own symptom patterns, and generally lasts for 4 weeks or more.

Some symptoms can help to differentiate the underlying cause of diarrhoea:

  • Offensive-smelling, watery and frothy stools may indicate the parasite Giardia lamblia
  • If diarrhoea occurs after overseas travel, it may indicate a parasitic infection
  • Stools that are thin, ribbon-like or pellets may indicate IBS or carcinoma
  • Bright red, profuse blood may indicate diverticulitis
  • Floating stools, pale in colour, and offensive-smelling may indicate malabsorption issues
  • Rapid heartbeat, unexplained weight loss, feeling shaky and clammy may indicate hyperthyroidism
  • A large volume of stool may indicate malabsorption issues, which may be linked to coeliac disease or laxative abuse
  • Family history may point towards lactose intolerance or coeliac disease
  • Onset of vigorous exercise may indicate exercise-induced diarrhoea

Get the best natural treatment for diarrhoea

What causes diarrhoea?

There are many underlying causes of chronic diarrhoea, which include:

  • Existing health conditions, such as IBS, IBD, colitis, microscopic colitis, coeliac disease, SIBO, ulcerating viral infections such as herpes simplex or cytomegalovirus, diverticulitis
  • Congenital or genetic disorders
  • Anxiety, chronic stress, trauma
  • Viral infections such as COVID-19 or HIV, norovirus, enteric adenoviruses, astrovirus, cytomegalovirus or viral hepatitis
  • Alcoholism, or excessive alcohol consumption
  • Post-surgery
  • Food intolerances and/or allergies
  • Medications such as antibiotics, non-osmotic laxatives, osmotic laxatives, antacids, sugar alcohols (mannitol, xylitol, sorbitol), and fat or carbohydrate-absorbing medications
  • Post-surgery, including resection or gastric bypass
  • Parasitic infections such as Giardia lamblia, Entamoeba or invasive bacterial infections, e.g. Salmonella spp., Clostridoides difficile or Tuberculosis yersiniosis or Tropheryma whippelii – Whipple disease
  • Inadequate bile acid, liver/gallbladder or pancreas dysfunction
  • Loss of gastric emptying due to dysfunction of peristalsis or migrating motor complex (a cleansing movement that occurs around every 90 minutes, when we are not digesting food)
  • Some cancers, or due to the treatment of some cancers
  • Excessive exercise, coffee, Vitamin C, magnesium
  • Nutrient deficiency, such as Vitamins B12, B2, and Vitamin A

Therefore, proper identification of the underlying cause of diarrhoea is important to establish effective treatment strategies of symptoms and underlying conditions, and rule out serious health conditions.

Treatment for diarrhoea – the conventional approach

Acute diarrhoea usually resolves quickly, provided patients maintain hydration and replace lost electrolytes. GPs may also prescribe bed rest, medications, and antibiotic treatment. In more severe cases/vulnerable people, hospitalisation with intravenous rehydration, antibiotic treatments, and antidiarrheal medications such as Loperamide (Imodium) or bismuth subsalicylate, and opioid derivatives diphenoxylate and dinenoxin may be required.

Diagnosis and treatment of chronic diarrhoea can be more complex with overlapping symptom pictures, particularly in long-standing cases, and in many conditions that include diarrhoea as a symptom. All cases of chronic diarrhoea create gut microbiome dysbiosis and intestinal hyperpermeability which may perpetuate diarrhoea, and extend treatment and recovery times.

Medications can have side effects, for example, antibiotic treatments which are non-selective antibacterial agents can disrupt the diversity and species make-up of the gut microbiome, killing beneficial as well as detrimental species which further can aggravate diarrhoea.

Testing may be used to identify/exclude parasites along with referrals for endoscopy and gastroscopy. GPs often don’t have the time in standard consultations for lengthy case taking, and therefore treatment either requires multiple visits or by trialling medications to reduce symptoms.

This process can take a long time and may be frustrating for patients, which is why many turn to functional medicine for alternative solutions.

Functional testing considerations for diarrhoea

Functional medicine practitioners use state-of-the-art testing to identify the underlying cause of diarrhoea, and this may indicate conditions such as IBS, IBD, coeliac disease, or SIBO, or a range of other conditions that have diarrhoea as a symptom.

Identifying the root cause directs the treatment plan, making them personalised, holistic, targeted and effective.

Testing might include:

  • Hydrogen/methane breath testing for SIBO
  • Food allergy, intolerance or sensitivities
  • Gut microbiome testing
  • Stool testing
  • Digestive function and nutrient absorption
  • Testing for parasites
  • Organic acids test
  • Other tests as required for your specific symptoms

 

Natural treatment for diarrhoea – the functional medicine approach

Our functional medicine-trained naturopaths at Melbourne Functional Medicine have a range of strategies for the treatment of diarrhoea.

Essential to identifying the root cause is the extensive investigation taken with each person with chronic diarrhoea. Our practitioners allow the time to properly dive into your medical case history, family health history, detailed investigation into the symptom picture, medications, diet, food allergies, nutritional deficiencies and environmental exposures.

Natural relief of diarrhoea symptoms may include a multifaceted approach, such as:

 

Dietary changes personalised to your case, which may include:

  • Eliminating food intolerances or allergy triggers
  • Including/increasing unprocessed whole foods to increase the range of prebiotic fibres for restoring/supporting diversity and species make-up of the microbiome
  • Including/increasing anti-inflammatory foods to reduce inflammation of the digestive system, or removal of specific foods that promote inflammation
  • Broths to restore and repair the gastrointestinal linings and help restore lost electrolytes

 

Lifestyle strategies may include: Stress resilience techniques like:

  • Shinrin-Yoku (forest bathing)
  • Meditation and mindfulness, breathwork, yoga or Tai Chi to reduce the impact of anxiety and stress on the digestive system

 

Precision probiotics: specific strains that will restore, support and increase diversity and make up of the microbiome, including:

 

Supplementation of depleted nutrients and those required for repairing and restoring the gut linings, and reducing inflammation, such as:

  • Electrolytes, magnesium, zinc, glutamine, Vitamin A, quercetin

 

Herbal medicines to soothe and tone the gut, heal gut linings and provide prebiotic fibre sources and polyphenols to support a healthy microbiome, such as:

  • Chamomile
  • Ginger
  • Turmeric (curcumin)
  • Agrimony
  • Marshmallow
  • Slippery Elm powder
  • Psyllium husk
  • PHGG
  • Barberry
  • Goldenseal
  • Oregon grape
  • Bilberry
  • Carob powder

As our functional medicine practitioners treat the whole person, strategies that aim to improve other aspects of health may also be included in your treatment plan. In our personalised program, your practitioner will work closely with you to direct your treatment, and your health coach will be your ongoing guide to help you implement your plan with greater ease. This approach has been helping people in Australia with chronic diarrhoea and other chronic health issues get well again.

Ready for a personalised, natural functional medicine treatment?

Our unique model of care was designed with you in mind. Find out how, then book a call today

Frequently

Asked

Questions

What are natural ways to stop diarrhoea?

The first step in treating diarrhoea naturally is identifying its cause, as this determines the right approach. Some helpful strategies include:

  • Acute cases (e.g., gastroenteritis): Let the body clear out the infection while staying well hydrated and replacing lost electrolytes. Seek medical attention if symptoms last longer than 24 hours or if dehydration occurs
  • Soothing remedies: Fresh ginger tea can reduce nausea, and slippery elm powder may calm gut inflammation, support the microbiome, and help restore the gut lining
  • Chronic diarrhoea: This often points to underlying issues such as food intolerances, microbiome imbalance, or gut inflammation. Working with a functional medicine-trained naturopath can uncover the root cause and guide personalised treatment

Why do I have diarrhoea?

Diarrhoea can have many different causes, ranging from short-term infections to ongoing digestive issues.

Common triggers include:

  • Infections (foodborne pathogens, contaminated water, or person-to-person spread) – often called gastroenteritis or food poisoning. Symptoms may include fever, chills, nausea, and vomiting
  • Food intolerances or allergies (e.g., lactose, gluten, FODMAPs)
  • Medications such as antibiotics or reflux medicines
  • Digestive disorders like IBS, IBD, or coeliac disease
  • Other health conditions that affect the gut or immune system

 

Acute diarrhoea is often infection-related. The biggest concern is dehydration, so if symptoms last more than 24 hours, seek immediate medical care.
Chronic diarrhoea (lasting 4+ weeks) is often a sign of an underlying condition. A functional medicine practitioner can help identify the root cause through testing and detailed assessment, then guide a natural treatment plan.

What causes constant diarrhoea?

Ongoing diarrhoea can have many possible causes. Some common factors include:

  • Food intolerances or allergies: such as lactose or gluten
  • Digestive conditions: including IBS, SIBO, coeliac disease, or IBD
  • Infections and parasites that disrupt gut balance
  • Nutrient imbalances or supplements: e.g., excess magnesium or Vitamin C
  • Lifestyle triggers: including high alcohol or caffeine intake, or intense exercise
  • Medications such as antibiotics or reflux medicines
  • Stress or anxiety, which can alter gut motility

Pinpointing what’s driving your symptoms is the first step – whether that’s food sensitivities, stress, or another digestive issue. Once identified, a clear plan can help you get back to feeling well.

What are the best foods for diarrhoea?

If you’re experiencing diarrhoea, diet can play an important role in soothing symptoms and supporting recovery.

Helpful foods and drinks include:

  • Broths: chicken, vegetable, or bone broth can restore fluids and electrolytes while providing collagen to help repair the gut lining
  • Bland foods: plain potatoes, rice, steamed vegetables, or dry crackers are often better tolerated
  • Herbal teas: ginger, chamomile, green tea, or black tea (without dairy) can be calming for digestion
  • Slippery elm powder: taken in water, this fibre helps soothe and protect the gut lining

Foods to avoid:

  • Sugary or processed foods
  • Spicy meals
  • Fatty or fried foods

Staying well hydrated is essential. If acute diarrhoea persists for more than 24 hours, seek medical assistance.

What is the best way to stop diarrhoea naturally?

The most effective way to stop diarrhoea is to understand what’s causing it. Common triggers include:

  • Other health conditions such as IBS, SIBO, or coeliac disease
  • Medications or supplements (e.g. magnesium, Vitamin C)
  • Lifestyle factors such as excessive alcohol, coffee, or intense exercise

Acute diarrhoea: If symptoms last longer than 24 hours, seek medical care to avoid dehydration.

Chronic diarrhoea: Natural approaches can be very effective when the underlying cause is identified. A functional medicine practitioner can assess your digestive health in detail and create a personalised plan that may include:

  • Nutritional support
  • Herbal medicines
  • Gut microbiome balancing
  • Lifestyle strategies for lasting relief

Can functional medicine treatment help diarrhoea?

Yes. Functional medicine takes a holistic approach to digestive health, aiming to identify and treat the root causes of diarrhoea rather than just masking symptoms.

A functional medicine practitioner may use:

  • Comprehensive case-taking to understand your health history and triggers
  • Functional testing to uncover food sensitivities, microbiome imbalances, or other underlying issues
  • Personalised treatment strategies that may include dietary adjustments, herbal medicine, probiotics, and lifestyle support

This natural, individualised approach can be effective for managing chronic diarrhoea and supporting long-term gut health.

Can stress or anxiety cause diarrhoea?

Yes. Stress activates the gut–brain axis and increases the release of stress hormones, which can speed up gut motility. This often results in diarrhoea, urgency, or abdominal cramping. Functional medicine approaches may include stress resilience practices such as meditation, deep breathing, or vagal nerve stimulation alongside digestive support.

Can probiotics help with diarrhoea?

Certain probiotic strains have been shown to reduce the frequency and duration of diarrhoea by restoring balance to the gut microbiome. However, not all probiotics are the same – the right strain matters. A practitioner can help identify whether probiotics are suitable for your type of diarrhoea, and if so, which strains may be most beneficial.

Can’t find what you’re looking for? Reach out to the team directly – we’ll be happy to assist.