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Taken back in 1884 by the administration of the Waters and Forests, the establishment is oriented towards the fish research with Jean Crettiez, then chooses the broader thematic of the Hydrobiology. From 1919, Louis Kreitmann, forest engineer Savoyard, founded the Hydrobiological Research Laboratory of Water and Forests. Until 1932, he carried out studies on the currents of Lake Geneva and endeavored to restore the fishing situation of this lake completely degraded by four years of poaching during the First World War.
In the continuity of his predecessor, Paul Vivier devoted much of his work to limnology, a science defined as the oceanography of lakes (a name given by the Swiss Forel 1841-1912), which became the oceanography of continental freshwaters. After the Second World War, it created the Station for Applied Hydrobiology, which consisted of four stations, including Thonon. The most important of these is the Paraclete, next to Amiens. One of them, Bernard Dussart, was appointed head of the Thonon-les-Bains laboratory until 1958, when Pierre Laurent was appointed.
In 1964, the forestry services are attached to INRA. It is then necessary to consider leaving the park of Rives because the premises become too small. It is also necessary to create a new fish experimentation tool. Until 1968, a vast estate on the shores of Lake Geneva is on sale, the INRA acquires. The current buildings are made and it was in 1975 that Raymond Février, then Director General of INRA, inaugurated the new premises built above the "castle", former property of Béguin sugar mills. Philippe Olive, Daniel Gerdeaux, Pierre Luquet and Gerard Balvay will then succeed to the direction of the station.
Since 1999, a Joint Research Unit (UMR-42) has been created between INRA and the University of Savoie.

It was run from March 2002 to December 2010 by Jean Marcel Dorioz, then from 2011 to 2017 by Bernard Montuelle

His current Director since January 2018 is Jean Guillard.