In 1898, he published the first book on underwater photography La Photographie sous-marine et les progrès de la photographie. Slides of his underwater photographs were shown at the 1900 Exposition Universelle in Paris.
In 1904, he was sent to Hanoi to investigate improvements to rice and the culture of pearl oysters. He returned to France in 1908. In 1910, he was named professor of zoology and animal physiology at the University of Bordeaux. In 1914 and 1916, Boutan and his brother worked on a diving suit for the French army. After the war, he began research into the artificial production of pearls, one of the first people to investigate this subject. In 1921, he was named director of the Station Biologique d'Arcachon. In 1924, he was named to the chair of general zoology of the faculty of science at the University of Algiers; he was also named director of the Station d’Aquaculture et de Pêches de Castiglione and inspector for the Algerian fisheries.
In 1929, he retired to Tigzirt in Algeria. He died there at the age of 75.