Abstract The average area-wide underground terrestrial water storage in the Kherlen River basin, a relatively pristine area in eastern Mongolia where human impacts have been minimal so far, has undergone a marked decline in the past decade; nevertheless, there is no evidence that any unusual or systematic long-term storage change has taken place over the past half century. This result follows from an analysis of daily streamflow records measured at three gauging stations on the river, namely at Baganuur, Undurkhaan and Choibalsaan. This absence of a clear trend in long-term groundwater storage is generally consistent with findings in previous studies regarding trends of other components of the hydrological cycle in Mongolia and neighbouring regions at similar latitudes, namely in northern Inner Mongolia to the east and Xinjiang to the west, and even further in the same direction in the adjacent areas of southern Central Asia of the Russian Federation and of Kazakhstan.