The Institute was established by the decision of the Governmental Commission for Foundation of the Czechoslovak Academy of Sciences on 29 April, 1952, which took effect on 1 January, 1953. Originally designated as the Laboratory of Water Management, it was later renamed the Institute of Water Management, and its present name dates from 1 January, 1958.

The first director was the founder of the Institute, Professor Jan Smetana (1953-1962), who was also one of the founders of the International Association of Hydrological Sciences (IAHS) and the International Association of Hydraulic Research (IAHR). The Institute was successively led by 9 directors: Ing. Václav Kolář, CSc. (1962-1967), prof. Ing. Pavel Novák, DrSc. (1967-1970), Ing. Radoš Smutek, CSc. (1970-1974), Ing. Atanas Curev, DrSc. (1974-1990), Ing. Alexander Puzanov, DrSc. (1990), Ing. Václav Eliáš, CSc. (1990-1997), prof. Ing. Pavel Vlasák, DrSc. (1997-2005), doc. Ing. Zdeněk Chára, CSc. (2005-2017) and now doc. RNDr. Martin Pivokonský, Ph.D.

At the beginning of its development, the Institute mainly solved classical problems of hydrodynamics related to waterworks and hydraulic structures, hydrology and problems of water treatment. As the water management, industry, health care and environment were developing, the main scope of the Institute was changing as well. In sixties and seventies, hydromechanics of Newtonian and non-Newtonian fluids, disperse and multi-phase systems, including rheology and biomechanics; transport and rainfall-runoff processes in river basins and environment protection were introduced into the research programme.

At the late 70s’ and during the 80s’ The Institute of Hydrodynamics of the Czechoslovak Academy of Sciences was divided into two sections which characterized the main research topics of the Institute. The section ‘Fluid Mechanics, Rheology and Transport Phenomena’ composed of the Department of Theoretical Hydrodynamics and Automatization of Experimental Activities, the Department of Transport Phenomena, the Department of Hydromechanics of Physicochemical Processes, the Department of Rheology of Anomalous Liquids, and the Department of Computational Techniques. The section ‘Disperse and Multi-Phase Systems’ composed of the Department of Disperse Systems, the Department of Fluid Biomechanics, and the Department of Hydrodynamics of Biosphere. Simultaneously an attention was paid to the ongoing computational technique and modernization of experimental equipment. This supported a passage from measurement of integral characteristics to the local and structural ones including their processing. In the topic of hydrodynamics of two- and multi-phase systems both radioisotopic measurement of local concentration and thermoanemometry for measurement of local velocity components were applied. However, the main emphasis was paid to the devices based on optoelectronic principles such as LDA (Laser Dopler Anemometry), PDA (Particle Dynamics Analyzer) for a determination of local velocity and turbulent characteristics, and also holography for visualization of kinetics of transport phenomena.

In the topic of fluid mechanics, research was oriented prevailingly to rheometry of industrially used liquids and polymers, rheology and modelling of hydrodynamics of suspensions in wellbore drilling, biorheology of blood properties and a reduction of inner friction in liquid flow by means of polymeric and micellar additives. In the topic of flow of disperse systems an attention was paid to sedimentation and densifying of suspensions, local flow characteristics of low-, medium- and high-concentrated fine-grained suspensions; research also continued in the system pipelines-liquid-capsules. At the turn of the 80s’ and 90s’ research was substantially strengthened in the topics of hydrology and environmental protection, widened by transport processes in the reservoirs, transport of water, pollutants and nutrients in non-saturated and saturated zones, and analyzing horizontal rainfalls and hydrology in mountainous catchments.

In 1993, after a separation of the former Czechoslovakia to the Czech Republic and the Slovak Republic, the Institute became a part of The Czech Academy of Sciences. In accord with Act No. 283/1992 Coll., on The Czech Academy of Sciences (CAS), and other legal regulations the Institute became a state budgetary, later contributary, organization. After reorganization at the beginning of 1993 the Institute was composed of two research departments: the Department of Mechanics of Fluids and Disperse Systems, and the Department of Hydrodynamics of Biosphere and Biomechanics (at present the Department of Hydrology and the Environment). The Department of Economy and Services carries out administrative, financial and workshop services. At present in accord with Act No 130/2002 Coll., on The support of research and development from public funds the Institute has been a public research organization (abbreviated as v. v. i.). Now research is dominantly oriented to the topics in Fluid MechanicsHydrologyRheology and Water Treatment Processes, which are applicable in their final phases in practice.