Batmanghelidj, often referred to as "Dr. Batman", or "Dr. B", attended Fettes College in Scotland in 1946. He graduated from St. Mary’s Hospital Medical School of London University, where he studied under Sir Alexander Fleming. His research in the field of gastroenterology, and subsequent books garnered media coverage in the nineties.

Batmanghelidj's medical practice in England ended when he relocated to Iran to help in the development of hospitals and medical centers.

In 1979, he was sent to the Evin Prison when the Iranian Revolution broke out. Charges were leveled against him, and he was scheduled to be executed. His execution was delayed so that he could serve as a resident doctor among the prisoners.

In 1982, he was released from prison, and later escaped from Iran and went to the United States to further his medical research.

Batmanghelidj states that he discovered the medicinal value of water during his prison stay by treating inmates with water when medication was not available. His methods and ideas ascribing common disease symptoms to dehydration have not been adopted by the medical community. The report of his findings was published as an editorial in the Journal of Clinical Gastroenterology, June 1983. The New York Times Science Watch reported this on June 21, 1983.

He authored Your Body's Many Cries for Water in 1992. In this book, Batmanghelidj asserts that chronic dehydration is the root cause of all physical diseases and explains the damaging effects of dehydration. He discusses the role of water in the body and his belief that water can transform the health needs of society. His writings related to the treatment of diseases and conditions with water have been considered controversial.

Batmanghelidji's writings have been translated into fifteen languages, and are sold in countries around the world. He died from complications related to pneumonia; a inflammatory condition of the lung, on November 15, 2004, in Virginia, U.S.A. His daughter Camila Batmanghelidjh is an award-winning social entrepreneur and psychotherapist who works with underprivileged children.

Dr Batmanghelidj's theories have been criticised by Dr Stephen Barrett M.D. on two main grounds, namely a lack of any documented peer-reviewed research and apparently exaggerated claims about the number of patients treated successfully.