The Institute of Hydrogeology and Hydrophysics named after U.M. Akhmedsafin was established by the decree of the Council of Ministers of the Kazakh SSR in 1965, based on the Department of Hydrogeology and Engineering Geology of the K.I. Satpayev Institute of Geological Sciences and the Department of Hydrogeology and Hydrothermal Studies of KazIMS of the USSR State Geological Committee.

In 1985, the institute was named after U.M. Akhmedsafin, an academician of the Kazakh SSR Academy of Sciences, Hero of Socialist Labor, and the first director and founder of hydrogeological scientific school in Kazakhstan.

In 2007, the Institute of Hydrogeology and Hydrophysics was renamed the Institute of Hydrogeology and Geoecology. By order No. 133 dated October 22, 2007, issued by JSC "Center of Earth Sciences, Metallurgy, and Enrichment" (CESME), the Limited Liability Partnership "Institute of Hydrogeology and Geoecology named after U.M. Akhmedsafin" was established as part of CESME.

Since 2016, the LLP "Institute of Hydrogeology and Geoecology named after U.M. Akhmedsafin" has been part of the Non-Commercial Joint Stock Company "Kazakh National Research Technical University named after K.I. Satpayev."

The Institute was founded by such renowned hydrogeologists as U.M. Akhmedsafin, Zh.S. Sydykov, S.M. Mukhamedzhanov, S.M. Shapiro, V.S. Zhevago, S.Zh. Zhaparhanov, K.M. Davletgaliyeva, V.F. Shlygina, M.Kh. Dzhabasov, R.M. Kurmangaliyev, Zh.V. Murtazin, V.N. Ivanov and others.

The institute established the first scientific school of arid hydrogeology in Kazakhstan, the developments of which formed the basis of several government decisions aimed at improving water supply in certain regions of the country. The data from groundwater forecasting assessments were used in the development of long-term programs for production hydrogeological studies, as well as in projects for the exploration and evaluation of groundwater reserves.