Bert also made a study of decompression sickness, suffered by deep-sea divers (who know its agonizing pain as “the bends”) when they are brought too quickly to the surface from the great pressures of the depths. Bert demonstrated that high external pressures force large quantities of atmospheric nitrogen to dissolve in the blood. During rapid decompression the nitrogen forms gas bubbles that obstruct capillaries. His classic La Pression barométrique, recherches de physiologie expérimentale (1878; Barometric Pressure: Researches in Experimental Physiology, 1943) was of fundamental importance to aviation medicine during World War II and to aerospace research in general.

An anticlerical leftist, Bert represented Yonne in the Chamber of Deputies (1872–86) and served as minister of education (1881–82) in Léon Gambetta's Cabinet. He was a proponent of French colonial policy in Indochina and was appointed governor general in Annam and Tonkin (1886). Despite his short tenure, his impact in Indochina was considerable. He took steps to liberalize French rule in the region, increasing the administrative role of the Vietnamese court and lessening the influence of the military in civil affairs. His various political and social reforms eased tensions in the area and served as a model for later French administrators.