The Society’s highest body of leadership is the general meeting of the Estonian Naturalists’ Society. To direct the Society’s activity, the general meeting elects a Board comprised of the president, two vice presidents, a secretary and three members of the Board. If necessary, additional members can be elected to the Board. The honorary president and the scientific secretary, who usually fulfils the role of the secretary, are also automatically members of the Board.
The majority of the Society’s work and activity takes place in sub-sections; the establishment of sections gained momentum from the 1920s onward, when a corresponding provision was included in the Society’s statutes. The sub-sections of the ENS consist of branches with the rights of sections (the Jakob von Uexküll Centre, the Estonian Theriology Society, the Estonian Malacology Society, the Estonian Mycological Society), specialised sections (geology, forestry, anthropology, theoretical biology, botany, entomology, the weather friends section and the lake committee) and committees (for the library, observation networks, history of natural sciences, environmental education, Estonian language ecological terminology, rare plants and Estonian language plant names). In addition, the Estonian assembly of ecology and the assembly of honorary members are active in the Society.