The history of the Institute of Hydrobiology started in 1909, when a small building of the Dnipro Biological Station appeared at the Trukhanov Island near the Kyiv. This one of the first in Europe Biological Station was organised by Kyiv Naturalists Association. Since stations foundations until events of 1917, the Dnipro Biological stations staff collected various material of different groups of aquatic organisms (plankton and benthic animals), carried out ornithological and parasitological study. Those studies were mainly regional faunistic and floristic, as well as study of some hydrobionts' groups composition and distribution near Kyiv.
Under total economic collapse and decay caused by The World War I, the station fell into neglect. The station resumed its work in 1919.
In 1921, the Dnipro Biological Station was included into the Academy of sciences of the UkrSSR. According to Decree of Presidium of the All-Ukrainian Academy of Sciences, on February 13, 1934 the Station was reorganised into the Hydrobiological Station. In May 1939, the assembly of the Academy of sciences of the Ukrainian SSR decided to rename the Hydrobiological Station into the Hydrobiological Institute
The governmental decision on the Institute of Hydrobiology organization was accepted in 1940 (Decree of the Peoples' Commissars Council of the UkrSSR # 696, of May 23, 1940).