Summary: Using baking soda for acid reflux is not only a folk remedy. Sodium bicarbonate is recommended by many doctors to help neutralize stomach acid. It can be problematic under certain circumstances.
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Using baking soda for acid reflux is an old folk remedy, but its value in treating heartburn has been verified by scientific fact. Baking soda, or sodium bicarbonate, is alkaline. When a small amount is mixed with water, it neutralizes refluxed stomach acid.  In fact, one popular effervescent antacid tablet has sodium bicarbonate as its main active ingredient. 
How to Use Baking Soda for Acid Reflux
According to the US National Library of Medicine, you should only use a half teaspoon of baking soda dissolved in a four-ounce glass of water when acid reflux occurs. The solution should be completely dissolved before ingesting. You should not ingest baking soda when overly full. It should never be administered to children. It is important that you do not ingest more than seven ½ teaspoons in a 24-hour period-no more than three ½ teaspoons if you are older than 60. Don't use for more than two weeks. 
Baking Soda Carries Potential Side Effects
Just because something is natural does always mean it is safe for everyone. The use of sodium bicarbonate should be supervised by a physician since it carries with it potential side effects. This is especially true for chronic ingestion.
Drug Interaction. Sodium bicarbonate may have interactions with other drugs.
Medical Condition Considerations. The use of sodium bicarbonate can cause problems when other health conditions exist such as appendicitis, intestinal bleeding, edema, heart disease, kidney disease, liver disease, problems with urination, or toxemia of pregnancy. 
Gastric Rupture. Though rare, gastric rupture has been reported as a side effect of sodium bicarbonate. When combined with gastric acid, it can cause excess gas release, which may cause a serious problem combined with excess food or liquid intake. 
High Blood Pressure Precaution
Each ½ teaspoon of baking soda contains 616mg of sodium.  Those with high blood pressure on sodium-restricted diets should not use sodium bicarbonate as an antacid unless prescribed by a physician.