This preliminary study highlights the vulnerability of water resources to mercury (Hg) contamination in the northern Indian plains, the global hotspot of atmospheric Hg emission. The total dissolved Hg in the river, lake and groundwater samples ranged from 5 to 1414 ng/L (n = 13). The dissolved Hg concentration increased by two orders of magnitude in the Gomati River due to the untreated effluent inputs from Lucknow urban center and by three fold in the Ganga River due to economic development during the last two decades. The dissolved Hg concentration in water resources was reported several folds high during the monsoon season and above the prescribed drinking water standards of World Health Organization. Atmospheric deposition was predominantly identified as source of Hg in the Karela Lake water (364 ng/L). The present study underscores the significance of monsoon-controlled anthroposphere-to-aquatic Hg transfer in the alluvial plain that acts as the caterer of 7% of the world’s population.