The Estonian Naturalists’ Society was founded on 10 October 1853 and is the oldest continually operating scientific society in the Baltic States. For the first 15 years, ENS was associated with the Livonian Society of Public Utility and Economy, and starting from 1878 with the University of Tartu. The presidents of ENS have been Carl Eduard von Liphardt, Karl Ernst von Baer, Edmund August Russow, Nikolai Ivanovitš Kuznetsov, Johannes Piiper, Paul Kogermann, Theodor Lippmaa, Eerik Kumari, Hans Trass, Erast Parmasto.

The majority of the Society’s activities take place in sections and committees. The first sub-section of the ENS to be established, in 1905, was the Commission of Lakes, which was the main centre for studying inland waters in Estonia until the Second World War, and it remains in operation to this day. At the same year, the library committee was also established, to facilitate putting the Society’s library in order; this committee is also in operation today. The Section on Nature Protection was created in 1920, the Section of Ornithology in 1921, the Section of Botany in 1928, the Tallinn branch in 1930, the Section of Geology in 1931, the Section of Entomology in 1937, the Section of Anthropology in 1939 and the Section of Physics and Chemistry in 1940. As of 2010, ENS has 23 sub-sections.

Starting from 1946 the ENS has been part of the Estonian Academy of Sciences. On 23 January 1998, an association agreement was signed between the Estonian Naturalists’ Society and the Estonian Academy of Sciences.