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The spatial distribution of permafrost and associated mean annual ground temperature (MAGT) and active layer thickness (ALT) are crucial data for hydrological studies. In this paper, we present the current state of knowledge on the spatial distribution of the permafrost properties of 29 river basins in Mongolia. The MAGT and ALT values are estimated by applying TTOP and Kudryavtsev methods. The main input of both methods is the spatially distributed surface temperature. We used the 8-day land surface temperature (LST) data from the day-and night-time Aqua and Terra images of the moderate resolution imaging spectroradiometer (MODIS). The gaps of the MODIS LST data were filled by spatial interpolation. Next, an LST model was developed based on 34 observational borehole data using a panel regression analysis (Baltagi, Econometric analysis of panel data, 3 edn, Wiley, New York, 2005). The model was applied for the whole country and covered the period from August 2012 to August 2013. The results show that the permafrost covers 26.3% of the country. The average MAGT and ALT for the permafrost region is − 1.6 °C and 3.1 m, respectively. The MAGT above -2 °C (warm permafrost) covers approximately 67% of the total permafrost area. The permafrost area and distribution in cold and warm permafrost varies highly over the country, in particular in regions where the river network is highly developed. High surface temperatures associated with climate change would result in changes of permafrost conditions, and, thus, would impact the surface water availability in these regions. The data on permafrost conditions presented in this paper can be used for further research on changes in the hydrological conditions of Mongolia.