In 1880 he traveled to Australia and brought back specimens of wildlife for the Natural History Museum. In 1883 he was appointed as an assistant to the famed marine biologist Professor De Lacaze - Duthiers at the Sorbonne. He organised a scientific expedition to study marine animals of the Red Sea in 1891.
His research into underwater photography took place in the Argo Laboratory in Banylus-Sur-Mer between 1892 and 1900. He became very proficient in using a Denayrouze diving helmet, and with his mechanic built three different underwater camera housings. Using plates specially manufactured by the Lumiere brothers Boutan produced the very earliest underwater photos taken by a diver. He developed various underwater lights and filters to improve his photography. In 1917, he and his brother developed a scuba system that worked with a deep sea diving helmet.
He published three different texts on underwater photography in 1894, 1898 and 1900. The third book was La Photographic Sous-marine et Les Progres de La Photographie, in which he predicted underwater photography for the masses. The International Scuba Diving Hall of Fame holds an original copy of this rare book it its collection.