The history of the Limnological Institute dates back to 1946, when Senator Dr. h. c. Dr. rer. nat. Walter Schlienz founded a privately financed Hydrobiological Station in the southern Black Forest, in Falkau, a small village between the lakes Schluchsee and Titisee. Schlienz had studied zoology, worked as a fisheries biologist, but soon turned to the fish processing industry. He became wealthy for inventing a system to instantly freeze fish while still on the fishing boat. However, he retained an interest in Hydrobiology - the science of life in water. He was thus a promoter of a newly branching research discipline within General Biology - Limnology as the science of inland waters - alongside Oceanology as subfields of Ecology. Three professors from Freiburg, among them the doyen of German limnologists, Prof. Dr. Robert Lauterborn, were godparents in the foundation of the station.
Dr. Hans-Joachim Elster, who had been head of the Institute for Lake Research and Lake Management in Langenargen until 1944, took over the management of the station in the Black Forest in 1948, which from then on was also called the Walter Schlienz Institute. In 1961 the station was affiliated with the University of Freiburg and one year later Germany's first chair of Limnology was established in Freiburg. Elster held this chair until his retirement in 1976. The hydrobiological station was renamed the Limnological Institute. The number of students and scientific staff around Prof. Elster soon exceeded the capacity of the station in Falkau, which at that time was housed in up to seven buildings - including an old farmhouse that had been converted into a laboratory building.
In the fall of 1970, Elster and his research group moved into a new building in Konstanz-Egg at Lake Constance, built on his initiative and thankfully financed by the Volkswagen Foundation. The new building was inaugurated in May 1971 as the Limnological Institute of the University of Freiburg. A new Limnological Institute was thus located on the shore of Lake Constance not far from the University of Konstanz, which had been founded shortly before, and into which the Institute was incorporated in 1981. Since then, lectures and courses are being offered to students from both Konstanz and Freiburg.
In 1978, Prof. Dr. Max Tilzer took over the chair of Limnology. In the same year, a professorship for Aquatic Zoology was established at the institute, held by Prof. Dr. Jürgen Schwörbel until his retirement in 1995. A second chair of Limnology was established in 1981 and filled by the microbiologist Prof. Dr. Norbert Pfennig. His laboratories were located on the university campus Gießberg in the biology building and not in the institute building at the lake. He was followed by Prof. Dr. Bernhard Schink in 1991 as Professor of Microbial Ecology, Limnology and General Microbiology.
After Prof. Dr. Tilzer became director of the Alfred-Wegener-Institute for Polar and Marine Research in 1992, the chair in Limnology remained vacant for some time, during which Dr. Meinhard Simon was temporary director of the institute. In 1996, Prof. Dr. Karl-Otto Rothhaupt became professor for Aquatic Ecology and head of the institute. Also in 1996, Prof. Dr. Reiner Eckmann took over the professorship in Aquatic Zoology.
In 2003 a professorship in Environmental Physics was established and filled with Prof. Dr. Frank Peeters.
Apart from many projects that were, and are being supported by third-party funds, the Institute carried out three major interdisciplinary research projects: the “Bodenseeprojekt” funded within the Priority Program of the German Research Foundation (DFG) from 1960 to 1968, the collaborative research centre (SFB) 248 “Cycling of Matter in Lake Constance” from 1986 until 1997, and the SFB 454 “Littoral Zone of Lake Constance” from 1998 until 2010. In addition, since 2017 the Institute is running the DFG Research Training Group (RTG) "R3 - Responses to biotic and abiotic Changes, Resilience and Reversibility of Lake Ecosystems" with more than 20 doctoral reserchers working on diverse topics related to the present, past and future of the Lake Constance ecosystem and its surroundings catchment area.
During its entire history, the Limnological Institute was an important research station and also the cradle of a large number of limnologists, ecologists and micobiologists, who serve or served as university professors or institute heads in Germany and abroad, among them: Jürgen Schwörbel (Univ. Konstanz), Uwe Tessenow (Univ. Ulm), Hartmut Kausch (Univ. Hamburg), Winfried Lampert (MPI for Limnology in Plön), Bruno Streit (Univ. Frankfurt), Bernhard Schink (Univ. Tübingen / Konstanz), Fritz Widdel (MPI Bremen), Walter Geller (UFZ Magdeburg), Heribert Cypionka (ICBM / Univ. Oldenburg), Norbert Walz (IGB Berlin), Ulrich Sommer (Geomar / Univ. Kiel), Thomas Weisse (Limnol. Inst., Mondsee, Austria), Jörg Overmann (TU Braunschweig / DSMZ), Reiner Eckmann (Univ. Konstanz), Meinhard Simon (ICBM / Univ. Oldenburg), Hans-Peter Grossart (IGB Berlin), Andreas Brune (MPI Marburg), Elisabeth Meyer (Univ. Münster), Jan-Ulrich Kreft (Univ. Birmingham, UK), Ursula Gaedke (Univ. Potsdam), Eric v. Elert (Univ. Köln), Rainer Meckenstock (Univ. Duisburg-Essen), Philipp Fischer (BAH Helgoland, Univ. Bremen), Andreas Kappler (Univ. Tübingen), Sabine Gerlach (Univ. Oldenburg), Elisabeth Gross (Univ. Lorraine, Metz, Frankreich), Andreas Lorke (Univ. Koblenz-Landau), Matthias Wantzen (Univ. Tours, France), Bodo Philipp (Univ. Münster), Karsten Rinke (UFZ Magdeburg), Alexander Wacker (Univ. Greifswald), Michael Pester (TU Braunschweig / DSMZ) and Dominik Martin-Creuzburg (BTU Cottbus-Senftenberg).
In 2018, Prof. Dr. Lutz Becks followed Prof. Dr. Rothhaupt as Professor of Aquatic Ecology and Evolution. Also in 2018, Prof. Dr. Christian Voolstra was appointed as Professor of Genetic Adaptation in Aquatic Systems, succeeding Prof. Dr. Eckmann. In addition, Jun.-Prof. Dr. Laura Epp joined the Limnological Institute as Junior Professor of Environmental Genomics in Aquatic Systems in 2018, and PD Dr. Dietmar Straile was consolidated with a working group on Plankton Food Web and Population Ecology. At the end of 2019, Prof. Dr. David Schleheck followed Prof. Dr. Schink as Professor of Microbial Ecology and Limnic Microbiology. In 2023, apl.-Prof. Dr. Alexander Brinker, head of the Fisheries Research Station Langenargen, is appointed to the Limnological Institute and the Department of Biology at the University of Konstanz with an associate professorship in Fish Ecology. In addition, Young Investigators Dr. Ana del Arco, Dr. Karla Martinez-Cruz and PD Dr. Nicolai Müller are active at the Institute with their own research projects.