Chronic watery diarrhea is often caused by viruses, bacteria or parasites from contaminated water or food and medications, such as antibiotics that disturb the intestines' balance of bacteria, explains Mayo Clinic. People who are lactose intolerant and exposed to dairy products may experience chronic diarrhea.
Chronic, watery diarrhea is also caused by allergies to certain foods, diseases of the intestines, laxatives, or alcohol abuse and diabetes, according to WebMD. People with an overactive thyroid can experience chronic diarrhea in addition to patients undergoing radiation therapy, surgery on the digestive system and those suffering from cancer. Vigorous exercise such as running can produce chronic, watery diarrhea.