Today's Institute of Aquatic Ecology and Fisheries Management was founded in 1928 as the "Fisheries Biological Station Weissenbach am Attersee" and at that time belonged to the University of Natural Resources and Applied Life Sciences.

After termination the Lectureship in 1934, the Fisheries Biological Station Weissenbach am Attersee was temporarily administered by the province of Upper Austria and taken over by the Federal Ministry of Agriculture and Forestry in 1936.

In 1944, the Fisheries Biological Station was placed under the control of the Institute for Fisheries (Berlin) as the "Department for Fisheries in Mountain Waters".

In the years 1947-1953 the two federal office buildings were erected in Scharfling. With the opening on 01.09.1953 the fish farm Kreuzstein, built by the Upper Austrian Chamber of Agriculture, was attached to the institute.

In the course of a regulation of the scope of duties of all federal agricultural institutes (Federal Institute Act 1983), the institute was renamed "Federal Institute of Fisheries Management".

After a further step of reorganization and task reform, the Institute was affiliated to the Federal Office of Water Management in 1995.

Since 2016, the Director's Office of the Federal Agency for Water Management has also moved from Vienna to Scharfling.