​​The Department was founded in 1953 as a result of the transformation of the Polish Academy of Sciences' fish farms into a research and production facility. Initially, it served as a field base for the Department of Aquatic Biology in Kraków, focusing on descriptive research. Carp breeding in this region has a long history, dating back approximately 400 years.

​As the Department developed a scientific foundation and a research team capable of independent studies, experimental research became the primary focus. The overarching goal was to conduct comprehensive research that yielded both theoretical and practical benefits. In the early years, the Department's research activities centered on understanding hydrobiont communities, physical and chemical processes, and the circulation of matter in ponds.

​Based on the Scientific Department of the Experimental Department of Ichthyobiology and Pond Management in Gołysz, the Department of Ichthyobiology and Pond Management of the Polish Academy of Sciences was established. This Department gained the status of a scientific institution of the Polish Academy of Sciences on July 1, 1992. On December 31, 2015, the Experimental Department was formally merged with the Department of Ichthyobiology and Fishery Management in Gołysz.

​In 2024, the Department achieved Good Laboratory Practice (GLP) certification for environmental toxicity testing of aquatic and terrestrial organisms. Obtaining this certificate confirms successful inspection by the Inspectors of the Bureau of Chemical Substances and our laboratory's adherence to GLP principles. It also guarantees the reliability of the test results we produce.