Chronic Constipation: The Real Causes and How to Fix It Naturally
By Joana Amram, Registered Nutritional Therapist & Naturopath (ANP) · Lisbon, Portugal
The standard advice for constipation — drink more water, eat more fibre, exercise — is not wrong. But for the significant proportion of people for whom it has made little or no difference, it is clearly not sufficient either.
Chronic constipation affects roughly 15% of the population. It is one of the most common reasons people visit a doctor, and one of the conditions where conventional medicine most often provides management rather than resolution. Laxatives help in the short term. They do not address why things stopped moving in the first place.
Understanding that reason is where lasting improvement becomes possible.
What Counts as Constipation?
Clinically, constipation is defined as fewer than three bowel movements per week, or stools that are consistently hard, lumpy, difficult to pass, or requiring straining. But in practice, "normal" varies considerably between individuals.
What I pay more attention to in clinical assessment is the full picture: the shape and consistency of stools (the Bristol Stool Scale is useful here), whether there is a sense of incomplete emptying, how long the issue has been present, and what has changed since symptoms began.
One thing I want to address directly: going once a day — or even once every two days — can be normal for some people if stools are easy to pass and complete. Going three times a day can also be normal. What is not normal is consistently hard stools, straining, pain, or a sense that the gut is simply not moving.
Why More Fibre Does Not Always Help
The first recommendation most people with constipation receive is to increase dietary fibre. This helps some people. For others, it makes things worse.
Here is why: fibre is fermented by bacteria in the large intestine. When the gut microbiome is dysbiotic — imbalanced toward gas-producing species — more fibre simply means more fermentation, more gas, more bloating, and often no improvement in transit time.
Additionally, in slow-transit constipation — where the fundamental problem is poor gut motility — adding more bulk to a gut that is not moving it creates more discomfort without resolving the underlying cause.
Fibre is valuable and important for long-term gut health. But it is not the solution to all types of constipation, and prescribing it without investigating the underlying driver is imprecise.
The Most Common Root Causes of Chronic Constipation
1. A Disrupted Migrating Motor Complex
The migrating motor complex (MMC) is the gut's housekeeping mechanism. Between meals, the gut performs a sweeping contraction that moves undigested residue, bacteria, and cellular debris toward the colon. This cycle occurs roughly every 90–120 minutes during fasting periods and is essential for normal gut motility.
The MMC only activates when you are not eating. Continuous snacking, grazing, or very frequent small meals suppresses the MMC and can significantly slow transit throughout the small intestine and colon.
This is one reason why structured meal timing — 3 proper meals per day with genuine fasting gaps between them — often produces dramatic improvements in constipation that no amount of fibre or laxatives achieves.
2. Hypothyroidism
The thyroid regulates the rate of metabolic processes throughout the body, including gut motility. An underactive thyroid — even subclinical hypothyroidism, where TSH is elevated but within the "normal" range — slows the entire digestive process.
This manifests as sluggish transit, hard stools, bloating, and chronic constipation that is entirely unresponsive to dietary interventions because the problem is hormonal, not dietary. Thyroid function should be assessed in anyone with persistent constipation that has not responded to other measures.
3. Dysbiosis and a Disrupted Microbiome
The gut microbiome directly influences gut motility. Specific bacterial species — including Lactobacillus and Bifidobacterium species — produce short-chain fatty acids that stimulate the enteric nervous system and promote peristalsis (the muscular contractions that move stool through the colon).
When these species are depleted — through antibiotic use, poor diet, chronic stress, or ageing — the signalling that drives colonic movement weakens. Methane-producing bacteria (an archaea called Methanobrevibacter smithii) are of particular clinical relevance: methane gas has been shown in research to slow intestinal transit directly, and high methane production in breath testing is strongly associated with constipation-predominant IBS.
4. Dehydration — But Not the Way You Think
Adequate hydration is important for stool consistency, but most people with chronic constipation are not meaningfully dehydrated. The more clinically relevant issue is when you are drinking water.
Drinking large amounts of fluid with meals can dilute digestive enzymes and stomach acid, impairing digestion. Drinking adequate water between meals — when digestion is not actively occurring — is what effectively contributes to stool hydration and ease of passage.
5. Low Stomach Acid
When stomach acid is insufficient, food is incompletely broken down before entering the small intestine. This impairs the cascade of digestive signalling that is supposed to follow — bile release, pancreatic enzyme secretion, and peristaltic contractions. The result can be sluggish transit throughout the digestive tract, not just the stomach.
6. Pelvic Floor Dysfunction
This cause is frequently overlooked and often presents as difficulty passing stool despite a reasonable urge — a feeling of blockage or incomplete evacuation. Paradoxical puborectalis contraction (where the pelvic floor muscle contracts when it should relax during defecation) is a mechanical cause of constipation that is not addressed by diet or supplements and requires specific pelvic floor physiotherapy.
If constipation is characterised primarily by difficulty passing stool even when frequency is adequate, pelvic floor assessment is worth considering.
7. Medications
Numerous medications cause or worsen constipation. The most common include: opioid analgesics, calcium channel blockers, iron supplements, antidepressants (particularly tricyclics), antacids containing calcium or aluminium, and antihistamines. A medication review is relevant in anyone with persistent constipation, particularly if onset correlated with starting a new drug.
8. Stress and the Nervous System
The enteric nervous system — the gut's own nervous network — operates semi-independently but is strongly influenced by the central nervous system via the vagus nerve. Chronic psychological stress activates the sympathetic nervous system (fight-or-flight), which suppresses digestive motility. The body redirects resources away from digestion when it perceives threat.
Many people with chronic stress find that their gut simply does not move well, regardless of what they eat. This is a physiological response, not a psychological weakness, and it requires nervous system support as part of treatment.
Natural Approaches That Actually Work
Meal Timing and Structure
Eating 3 structured meals per day with 4–5 hour gaps, no grazing between them, is one of the most clinically effective interventions I use for constipation. It allows the MMC to run between meals and re-establishes the digestive rhythm that the gut needs.
This change alone, consistently applied, significantly improves constipation in a large proportion of people — without a single supplement.
Movement After Meals
A 10-minute walk after meals accelerates gastric emptying and promotes colonic motility. This is well-documented and free.
Magnesium
Magnesium — particularly in the forms of magnesium citrate or magnesium glycinate — is a highly effective and well-tolerated support for constipation. It draws water into the colon osmotically (citrate more so) and supports muscular relaxation in the gut wall. Unlike stimulant laxatives, it is not habit-forming and does not cause dependency.
Addressing Dysbiosis
When methane-producing bacteria are identified as a driver — often through a breath test or by the pattern of severe constipation with significant bloating — targeted antimicrobial treatment followed by microbiome rebuilding produces results that fibre and hydration alone cannot.
Supporting Thyroid Function
If hypothyroidism is a factor, supporting thyroid health through nutrition (adequate iodine, selenium, zinc, and iron), stress reduction, and medical management where appropriate is foundational.
The Squatting Position
Anatomically, the human colon is designed to empty most efficiently in a squatting position, which straightens the anorectal angle and reduces the effort needed to pass stool. A small footstool elevating the feet while on the toilet (raising the knees above hip level) replicates this position. This simple change produces meaningful improvement in ease of defecation for many people.
What Chronic Constipation Can Mean Long-Term
Beyond discomfort, chronic constipation has implications for gut health that extend further. Slow transit means that waste products and bile acids remain in contact with the colon mucosa for longer, increasing inflammatory load. The microbiome of chronically constipated individuals is measurably less diverse and less abundant in beneficial species.
Addressing constipation is not just about comfort — it is about reducing the long-term inflammatory burden on the gut and maintaining a healthy microbiome environment.
Joana Amram is a registered Nutritional Therapist and Naturopath accredited by the ANP (Association of Naturopathic Practitioners) and trained at the College of Naturopathic Medicine in London. She specialises in gut health, IBS, SIBO, microbiome balance, and digestive disorders. Consultations available online worldwide and in-person in Lisbon, Portugal, in English, Portuguese, Spanish, and French.
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Disclaimer: This article is for educational purposes only and does not constitute medical advice. Please consult a qualified healthcare practitioner for personalised recommendations.