6 Causes of Fishy-smelling Watery Diarrhea.

Our content is not intended nor recommended as a substitute for medical advice by your doctor. Use for informational purposes only.

Fishy-smelling watery diarrhea is often due to acute infection (giardiasis, viral, or bacterial gastroenteritis). However, chronic offensive stools can result from conditions such as celiac disease, chronic giardiasis, food intolerance, etc.

The following are the common causes of fishy-smelling watery stools:

A. Acute fishy-smelling watery diarrhea.

1 . Giardia infection.

Giardia is protozoa that commonly cause watery diarrhea with a fishy or foul smell. The characteristic bad odor from giardiasis results from fat malabsorption.

You get a giardia infection via contaminated foods or drinks. The organism mainly infects your small intestine leading to the destruction of its lining with subsequent malabsorption.

Giardiasis can be both acute and chronic. And it is more common in:

  • International travelers and adopters.
  • Children under the age of 6.
  • Older people.
  • Patients with low immunity (as with those taking chemotherapy).

How common?

Giardia lamblia is the third most common cause of acute diarrhea (after rotavirus and cryptosporidium). An estimated 300 million cases are reported each year worldwide.

75% of people with acute giardiasis have fishy-smelling watery diarrhea. Moreover, people with chronic giardiasis are also likely to have fishy or foul-smelling diarrhea.


The sym[toms develop 7 to 14 days after consuming contaminated foods or drinks (reference).

The following are the common symptoms of acute giardiasis and their relative frequency (reference).

  • Acute onset diarrhea (greasy, yellowish, or light brown).
  • Sudden abdominal cramps and pain.
  • Foul or fishy-smelly watery diarrhea occurs in up to 75% of cases of acute giardiasis.
  • Malaise and fatigue (in 86% of the cases).
  • Bloating.
  • Flatulence and excess gas.
  • Nausea (69%).
  • Vomiting (in 23%).
  • Fever in 15%.
  • Sometimes, constipation.
  • Skin itching (urticaria).
  • Many people may get giardiasis infection without any symptoms.
  • The symptoms (including fishy-smelling watery diarrhea) often last one to four weeks.


  • Drink plenty of fluids.
  • Avoid high-fat foods.
  • Eat bland, easy-to-digest foods such as the BRAT diet (bananas, rice, apple sauce, and toast).
  • Anti-protozoal medication such as Tinidazole, nitazoxanide, or metronidazole (Flagyl®).
  • OTC medicine to stop diarrhea, fever, and abdominal pain may also help in severe cases.
  • Giardiasis may become chronic in some patients; a visit to your doctor is essential if you have symptoms consistent with

2. Viral Gastroenteritis

Viral gastroenteritis is very common (more common than giardiasis). Up to 70% of acute infectious diarrhea cases are due to viruses (reference). The most common viruses include:

  • Norovirus (most common).
  • Rotavirus (less common nowadays due to vaccination).
  • Adenoviruses and others.

Viral gastroenteritis is also known as (stomach flu) because it causes:

  • Acute onset watery diarrhea (sometimes with a fishy-smelling), nausea, and vomiting.
  • Flu-like symptoms such as low-grade fever, headaches, body aches, etc.

It isn’t easy to differentiate between giardiasis and viral gastroenteritis. However, viral gastroenteritis is often milder.

Unlike giardiasis (which lasts for one to four weeks), Stomach flu often lasts for a few days.

Also, body aches are more prominent with viral gastroenteritis.

Treatment of viral gastroenteritis:

Until now, no medication directly destroys stomach viruses. The treatment is mainly supportive until the diarrhea resolves.

  • Stomach rest (stop eating solid foods for a few hours and stay on liquids).
  • Rest.
  • Good hydration (drink plenty of fluids).
  • Eat bland, easy-to-digest foods (such as the BRAT diet).
  • OTC medications may be needed to stop diarrhea, abdominal pain, and vomiting.

3. Bacterial gastroenteritis.

Bacteria also can cause severe clear or watery diarrhea with fishy-smelling stool. However, they commonly cause dysentery (scanty diarrhea with mucus and blood).

Bacteria cause a more severe form of digestive system infections. The common causes include (reference ):

  • Campylobacter.
  • Shigella (causes bacillary dysentery).
  • E. Coli.
  • Salmonella.

Bacteria and their toxins are common causes of food-borne illnesses (food poisoning.


  • Often in the form of dysentery (scanty diarrhea with blood and mucus).
  • It also can be in the form of fishy-smelling, watery diarrhea.
  • Severe abdominal pain and cramps (more extreme than viral gastroenteritis).
  • Tenesmus (persistent urge to poop, but only mucus or blood comes out).
  • Fever is often of high grade.
  • Anorexia is common. However, vomiting is less prominent than viral gastroenteritis.
  • More severe systemic symptoms such as headache, high-grade fever, and chills.
  • Dehydration may occur in severe cases (extreme thirst, peeing too little, confusion, etc.).

The type of gastroenteritis (viral, bacterial, or protozoal) is often challenging to differentiate on a symptom basis. Usually, your doctor will require a stool sample to determine the cause.


  • The same as viral gastroenteritis (rest, good hydration, and bland foods).
  • Antibiotics may be needed when the symptoms are severe.

4. Other causes of acute (new) onset fishy-smelling watery diarrhea:

The following are other possible causes of acute fishy stool (with or without watery diarrhea):

  • Overeating high-sulfur foods such as meats, garlic, broccoli, kale, and cabbage.
  • Recent drug use (especially antibiotics).
  • Blackish blood in the stool (as with peptic ulcer bleeding) may also cause fishy-smelling diarrhea.

B. Chronic/recurrent  Fishy-smelling watery diarrhea.

1 . Celiac disease.

Celiac disease is a chronic disease making your intestine unable to absorb food properly (malabsorption). It is caused by an allergy to (gluten), a protein found in wheat, rye, and barley.

Celiac disease often starts between 20 and 30 years but can begin at any age. It affects about 1 to 1.5% of the world’s population (reference).

The symptoms include:

  • Chronic foul or fishy-smelling diarrhea due to malabsorption.
  • The stool is often watery or loose.
  • Weight loss.
  • Anemia (easy fatigue, headache, dizziness, fast heartbeats, and shortness of breath).
  • Skin rashes.
  • Red-glazed tongue.
  • Bony pain and easy fractures.

Celiac disease is often diagnosed by either blood tests (such as serum TTG) or by taking a biopsy from your intestinal wall via endoscopy.

Once diagnosed, a Gluten-free diet will reverse all the effects of celiac disease (including the fishy-smelling watery diarrhea).

2. Chronic pancreatitis.

Inflammation of the pancreas can be either acute or chronic. The Chronic inflammation of the pancreas results from a variety of causes, such as:

  • Chronic alcoholism.
  • Smoking.
  • Increased blood lipids (triglycerides).
  • Autoimmune.
  • And others.

The pancreas exerts most digestive enzymes, such as lipase, amylase, and trypsin.

With chronic pancreatitis, the destruction of its tissues leads to a deficiency of such enzymes. Chronic pancreatitis leads to a condition called (Exocrine pancreatic insufficiency) which causes malabsorption.

The malabsorption is responsible for chronic watery diarrhea and characteristic foul or fishy smell due to fat malabsorption.

Learn More about acute pancreatitis.

3. Chronic infections.

Some infections of the digestive system may also cause fishy-smelling stool. Common examples include:

  • Chronic giardiasis.
  • Clostridium difficile infection.
  • E-coli.
  • Salmonella (typhoid fever).

The most common symptoms are chronic fishy-smelling diarrhea, low-grade fever, and abdominal pain.

The diagnosis is often complicated and requires stool or blood testing to detect the organism.

4. Food intolerance.

Food intolerance is a common cause of chronic or recurrent fishy-smelling watery diarrhea.

Food intolerance occurs when your digestive system becomes unable to digest certain foods.

The most common forms of food intolerance are:

  • Lactose intolerance (in milk and dairy products).
  • FODMAP intolerance (in patients with irritable bowel syndrome).
  • Fructose intolerance: found in most fruits and honey.
  • Other less common forms include amines, caffeine, salicylates, and others.

Food intolerance symptoms start shortly after eating the offending foods. The most common symptoms include:

  • Excess gas and flatulence.
  • Loose or watery stool.
  • Offensive or fishy-smelling diarrhea.
  • Abdominal pain.
  • Nausea and anorexia.
  • Vomiting may occur in severe cases.

Learn more about food intolerance.

5. Other causes of chronic foul-smelling diarrhea:

  • Irritable bowel syndrome.
  • Crohn’s disease.
  • Ulcerative colitis.
  • Bile acid diarrhea.
  • Small intestinal bacterial overgrowth.
  • Chronic use of medications such as proton pump inhibitors.
  • Other malabsorption syndromes such as tropical sprue and Whipple’s disease.

When to see a doctor for fishy-smelling, watery diarrhea:

  • Acute onset of severe or persistent diarrhea.
  • Blood in stool.
  • Extreme abdominal pain.
  • Chronic watery diarrhea of unknown cause.
  • Weight loss.
  • High-grade fever.
  • Prolonged diarrhea for more than three days.
  • Persistent vomiting.
  • Signs of dehydration include confusion, dizziness, extreme thirst, and fast heartbeats.