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Van Helmont, who came from a noble Brussels family, was educated at the Catholic University of Louvain in medicine, mysticism, and chemistry, but declined a degree from them. Rejecting all offers of employment he devoted himself to private research at his home. In 1621 he was involved in a controversy with the Church over the belief that it was possible to heal a wound caused by a weapon by treating the weapon rather than the wound. Van Helmont did not reject this common belief but insisted that it was a natural phenomenon containing no supernatural elements. He was arrested, eventually allowed to remain under house arrest, and forbidden to publish without the prior consent of the Church. He wrote extensively and after his death his collected papers were published by his son as the Ortus medicinae (1648; Origin of Medicine).

Van Helmont rejected the works of the ancients, although he did believe in the philosopher's stone. He carried out careful observations and measurements, which led him to discover the elementary nature of water. He regarded water as the chief constituent of matter. He pointed out that fish were nourished by water and that substantial bodies could be reduced to water by dissolving them in acid. To demonstrate his theory he performed a famous experiment in which he grew a willow tree over a period of five years in a measured quantity of earth. The tree increased its weight by 164 pounds despite the fact that only water was added to it. The soil had decreased by only a few ounces.

Van Helmont also introduced the term ‘gas’ into the language, deriving it from the Greek for chaos. When a substance is burned it is reduced to its formative agent and its gas and van Helmont believed that when 62 pounds of wood is burned to an ash weighing 1 pound, 61 pounds have escaped as water or gas. Different substances give off different gases when consumed and van Helmont identified four gases, which he named gas carbonum, two kinds of gas sylvester, and gas pingue. These we would now call carbon dioxide, carbon monoxide, nitrous oxide, and methane.