In summer (pre-monsoon) of recent years, low water level among the last few decades, has been observed in several lower Indian reaches of the Ganges (or Ganga) river (with estimated river water level depletion rates at the range of -0.5 to -38.1 cm/year between summers of 1999 and 2013 in the studied reaches). Here, we show this Ganges river depletion is related to groundwater baseflow reduction caused by ongoing observed groundwater storage depletion in the adjoining Gangetic aquifers (Ganges basin, -0.30 ± 0.07 cm/year or -2.39 ± 0.56 km3/year). Our estimates show, 2016-baseflow amount (~1.0 × 106 m3/d) has reduced by ~59%, from the beginning of the irrigation-pumping age of 1970s (2.4 × 106 m3/d) in some of the lower reaches. The net Ganges river water reduction could jeopardize domestic water supply, irrigation water requirements, river transport, ecology etc. of densely populated northern Indian plains. River water reduction has direct impact on food production indicating vulnerability to more than 100 million of the population residing in the region. The results of this study could be used to decipher the groundwater-linked river water depletion as well as the regional water security in other densely populated parts of the globe.