Do Fish Oil Pills Make You Use the Bathroom? Understanding Digestive Side Effects

January 6, 2026 •

3 min read

According to the National Institutes of Health, fish oil is one of the most widely used dietary supplements in the United States, yet for some, it comes with unwanted digestive effects. Many people who start taking omega-3 supplements often wonder, "Do fish oil pills make you use the bathroom more often?" The short answer is yes, and it's a common side effect for certain individuals.

Quick Summary

Fish oil supplements can cause gastrointestinal side effects like diarrhea, loose stools, and bloating, particularly with high doses. The high-fat content can act as a laxative and overwhelm the digestive system. Taking supplements with food and adjusting dosage can help manage these issues.

Key Points

Dosage is Key: High doses of fish oil, typically over 3 grams daily, are more likely to cause diarrhea and loose stools.
Fat Content's Role: The high-fat concentration in fish oil can act as a lubricant and laxative, speeding up intestinal transit.
Absorption Matters: Unabsorbed oil in the digestive tract can draw excess water into the colon, resulting in looser bowel movements.
Strategize Your Intake: Taking fish oil with a meal, splitting the dose, or choosing an enteric-coated option can significantly reduce digestive side effects.
Long-Term Gut Health: While initial side effects can occur, omega-3s have shown the potential to improve gut microbiome diversity and reduce inflammation over time.
Consult a Professional: If side effects persist despite adjustments, it's important to consult a healthcare provider to rule out other issues and discuss alternatives.

Why Fish Oil Can Cause Digestive Problems

The gastrointestinal side effects associated with fish oil, such as diarrhea and loose stools, are primarily due to its high-fat content. The body's digestive system can be sensitive to large doses of fat, especially if it's introduced suddenly. Omega-3 fatty acids, which are fat-soluble, require dietary fat for optimal absorption. Without sufficient accompanying fat, the oil can float on top of the stomach contents, leading to indigestion, acid reflux, and discomfort. This unabsorbed oil can then travel to the colon, drawing water into the intestines and stimulating bowel movements, which can cause loose stools or diarrhea.

The Role of Dosage

Research indicates that digestive issues become more common when an individual takes higher doses of fish oil. For instance, reports of diarrhea are most frequent among those consuming over 3 grams of fish oil daily. This is often the threshold where the body's ability to efficiently process the concentrated fat becomes overwhelmed, triggering a laxative effect. By starting with a lower dosage and gradually increasing it, the body can adapt, and side effects may be minimized.

How to Minimize Gastrointestinal Side Effects

If you experience digestive discomfort from fish oil, several simple strategies can help alleviate the problem:

Take with food: Consuming your fish oil supplement with a meal, particularly one containing healthy fats, significantly improves absorption and can prevent the oil from floating in the stomach.
Split the dose: If your daily intake is high, dividing the dose into two smaller amounts and taking them with different meals (e.g., breakfast and dinner) can reduce the strain on your digestive system.
Try enteric-coated capsules: These capsules are designed to bypass the stomach and dissolve in the small intestine, which can prevent issues like fishy burps and acid reflux.
Freeze the capsules: Freezing your fish oil capsules can slow down the digestion process, helping the capsule get further along your digestive tract before it breaks down.
Switch to a different source: Alternatives like krill oil or algae oil might be better tolerated by some individuals. Krill oil, for example, is often better absorbed and may cause fewer digestive issues.

Fish Oil Formulations and Digestive Impact


Feature	Standard Fish Oil	Enteric-Coated Fish Oil	Krill Oil
Digestive Sensitivity	Higher risk of gas, burps, and reflux	Lower risk of upper GI side effects	Generally well-tolerated, less fishy aftertaste
Absorption	Enhanced when taken with food	Delayed until the small intestine	Often better absorbed due to phospholipid form
Dosage Management	May need to split high doses	Can be taken in a single dose	Often effective at lower doses
Primary Cause of GI Distress	High fat content and poor stomach absorption	Large volume of oil released at once	Infrequent; potentially due to individual sensitivity

Fish Oil and the Gut Microbiome

Beyond just causing temporary digestive discomfort, omega-3 fatty acids have a more profound, and often positive, relationship with gut health. Studies have shown that omega-3s can shape microbial communities in the gastrointestinal tract. For example, they may increase the diversity of the gut microbiome, which is associated with better overall health outcomes. Omega-3s also promote the growth of beneficial bacteria and strengthen the intestinal barrier, which can be helpful for those with inflammatory bowel diseases. While the specific impact varies by individual and dosage, there's evidence that, over time, fish oil can contribute to a healthier gut environment, despite initial gastrointestinal side effects.

Conclusion

In summary, experiencing changes in bowel habits, such as loose stools or diarrhea, from fish oil pills is a documented and fairly common side effect, especially when taking a high dose. The primary culprit is the high-fat concentration, which can overwhelm the digestive system and act as a laxative. The good news is that these side effects are often manageable by adjusting your routine. By taking your supplement with a meal, splitting the dose, or opting for an enteric-coated formula, many individuals can avoid the unpleasant bathroom side effects and continue to reap the health benefits of omega-3s. Consistency is more important than timing, so find a routine that works best for your body. As with any supplement, if side effects persist or worsen, it's always best to consult with a healthcare professional to explore other options or address any underlying issues.

For more information on digestive wellness, you can visit the National Institute of Diabetes and Digestive and Kidney Diseases at https://www.niddk.nih.gov/health-information/digestive-diseases.

Frequently Asked Questions

Fish oil contains a high concentration of fat. At higher doses, this fat can overwhelm the body’s digestive system, leading to poor absorption. The unabsorbed fat acts like a lubricant and draws water into the intestines, which can result in loose stools or diarrhea.

To prevent diarrhea, try taking your fish oil supplement with a meal, especially one containing other fats. You can also split your daily dose into smaller amounts throughout the day. Using an enteric-coated formula or starting with a lower dose can also help.

The timing is less important than taking it with food. Taking fish oil with your largest meal of the day, which is often dinner, can improve absorption and reduce the risk of reflux. Splitting your dose between morning and evening meals can also be effective.

While it's technically possible, taking fish oil on an empty stomach is more likely to cause side effects like acid reflux, burping, and general stomach upset. It is generally recommended to take it with a meal to improve absorption and minimize digestive discomfort.

Not necessarily. Digestive upset is a common side effect of fish oil itself, especially at high dosages. However, ensuring you have a high-quality, non-rancid product from a reputable source is always a good idea, as poor quality can contribute to side effects.

Yes, research suggests that omega-3 fatty acids can positively influence the gut microbiome by increasing microbial diversity and potentially reducing inflammation over time. Initial digestive upset is a distinct issue from the long-term effects on the gut environment.

You should consult a healthcare professional if digestive side effects like diarrhea persist for more than a day or two after adjusting your dose or timing. They can help rule out other health issues and discuss alternative supplement options.