IL RAS was founded by the Decree of the Presidium of the USSR Academy of Sciences of July 29, 1971 No. 731 based on the Laboratory of Limnology that was originated in 1944 at the Department of Geological and Geographical Sciences of the USSR Academy of Sciences.

Based on the Decree of the President of the RSFSR of November 21, 1991 No. 228 "On the organization of the Russian Academy of Sciences", IL RAS became a part of the Russian Academy of Sciences as the Institute of Limnology of the Russian Academy of Sciences.

In compliance with the Decree of the Presidium of the Russian Academy of Sciences dated December 18, 2007, No. 274 IL RAS was renamed to the Institution of the Russian Academy of Sciences: Institute of Limnology RAS.

By the decree of the Presidium of the Russian Academy of Sciences dated December 13, 2011 No. 262, the IL RAS was renamed into the Federal State Institution of Science: Institute of Limnology of the Russian Academy of Sciences.

In compliance with the Federal Law "On the Russian Academy of Sciences, reorganization of State Academies of Sciences and amendments to certain legislative acts of the Russian Federation” of September 27, 2013 No. 253-ФЗ and Decree of the Government of the Russian Federation of December 30, 2013 No. 2591-p IL RAS was turned over to the management of the Federal Agency for Scientific Organizations.

By the Decree of the Russian Federation President of May 15, 2018 No. 215: “On the structure of Federal Executive Authorities” and by the Order of the Russian Government of June 27, 2018 No. 1293-р IL RAS is transferred to The Ministry of Science and Higher Education of the Russian Federation management.

In accordance with the Order of The Ministry of Science and Higher Education of the Russian Federation of December 18, 2019 No. 1399 IL RAS became a separate division of the St. Petersburg Federal Research Center of the Russian Academy of Sciences.

The Institute is a leading limnology research institution of Russia doing basic and applied research in limnology; developing methods intended for in-depth comprehensive study of the structural and functional features of lake ecosystems, restoration of lakes and reservoirs, their use for drinking water supply purposes, fish farming and recreation; solving lakes’ monitoring and managing problems as well as tasks of their natural resources’ rational use.