In July 1987, Lower Saxony’s minister of Science and Art approved the establishment of the ICBM as a cooperation of the university departments of mathematics, biology, physics and chemistry. In 1991, the ICBM was approved as a central organisation of the University of Oldenburg. The registered association „Centre for Research on Shallow seas, Coastal Zones and the Marine Environment – Research Centre Terramare” (Zentrum für Flachmeer-, Küsten- und Meeresumweltforschung e.V. – Forschungszentrum Terramare) which was founded in 1990 in Wilhelmshaven and financed through federal state resources was incorporated into the ICBM in 2008.
The former directors of the ICBM are Wolfgang Krumbein, Ulrich Kattmann, Hans Joachim Schellnhuber, Bruno Eckhardt, Wolfgang Ebenhöh, Heribert Cypionka, Meinhard Simon, Hans-Jürgen Brumsack, Ulrike Feudel,  Jürgen Rullkötter, Helmut Hillebrand, Bernd Blasius and Oliver Zielinski. At present, the institute is headed by Heinz Wilkes.