Beginning in 1848, the eastern sector was turned into the hospital sector while the western sector was reserved for people under observation. As a result of this division, sick people could be kept separated from health people and the risk of contagion could be reduced. In addition, by confining sick people to the eastern sector, the idea was to allow the prevailing westerly winds to blow "miasmas" out over the river and not over healthy people. According to the beliefs of the time, miasmas - putrid, invisible, free-floating particles - attacked bad Christians and people of loose morals. At the time when the quarantine station first went into operation, few doctors practiced what today would be considered a scientific type of medicine - i.e., based on "contagionist" principles; the majority tended instead to hold to a dogmatic type of medicine. Modern medicine really came into its own in the 1870s,
thanks to the discoveries of Louis Pasteur and Robert Koch and to improvements in the microscope.
In 1869, Dr. Frédérick Montizambert took over as the station's third superintendent. During the subsequent 30 years, he would travel around the world, tour various quarantine stations, and implement the best techniques in Canada. Montizambert modified the quarantine process and made the Grosse Île station a leading-edge facility for its time.
The 1880s were particularly decisive for the future of the station. Work was begun constructing a brick hospital in 1881. As of 1886, incoming ships were systematically disinfected and fumigated. Year 1893 saw the completion of the disinfection building, designed to handle both immigrants and their baggage. Finally, in response to the 
growing requirements of maritime transport companies, a hotel for cabin passengers was built in 1893.
With the arrival in 1899 of Georges-Élie Martineau, Montizambert's successor and the last quarantine station superintendent, modernization of the island continued, particularly through the advent of electricity in 1902. Under Martineau's supervision, the station was equipped with a vaccination and medical inspection office along with a bacteriological laboratory, a first-class hotel and a third-class hotel.
