At the suggestion of the academician Endre Dudich, The Hungarian Academy of Sciences (MTA) in cooperation with the Eötvös Loránd University established a joint research team in 1957. This research group was named, which was quite unconventional at those days, the Danube Research Station of the Hungarian Academy of Sciences (MTA) and it was operated this way until 1976.
From 1977 retaining its name, the Danube Research Station of the HAS continued its activity as a department of the Institute of Botany of the HAS (the name was changed to Institute of Ecology and Botany of the HAS in 1984). The leaders of the Station were: Endre Dudich (1957-1969), Gábor Szemes (1970-1972), Árpád Berczik (1973-1999) and in the period from 2000 to 2010 Nándor Oertel and Tihamér Keve Kiss alternately.
In 2010, the 180th General Assembly with the leadership of its president, József Pálinkás, decided to improve the Station to an independent research institute, thus the Danube Research Institute was established in 2011 (the founding commissioner and later director was Gábor Guti).
As a renewal of the research network of the HAS, the Centre for Ecological Research was established in 2012 (Centre for Ecological Research of the HAS, director-general: András Báldi) and the Danube Research Institute was involved in it. Beside the director-general post, András Báldi received the director position of the Danube Research Institute in 2013, but the directional tasks were given to Attila Engloner. In 2016, Attila Engloner became the appointed director of the institute. Intensive infrastructure and human resource development was implemented, which significantly increased the scientific performance of DRI.
Three departments were set up within DRI: the Department of Hydro- and Plant Ecology, the Department of Restoration and Animal Ecology, and the Department of Tisza River Research, that latter was redirected from the Balaton Limnological Institute of HAS in favour of the thematic centralisation of stream research.
The problem of the proper placement of the Danube Research Institute lasted many years and finally was solved in 2014. All of the colleagues working in different places (Göd, Vácrátót and in several places in Budapest) were finally moved into the headquarters of the Institute at Karolina street in Budapest. The Department of Tisza River Research gained appropriate location in Debrecen at the Institute of Nuclear Research of HAS.
In order to efficiently organize and manage the research work, the establishment of research groups has also begun.
From the 1st of April 2019, Zsolt Végvári, DSc became the director of the Danube Research Institute.