Ganga, a river of global significance, is under increasing pressure from excessive release of carbon and nutrients. We conducted the first detailed watershed-scale study to assess water quality status and possible drivers in different segments of the Ganga River. For this, we analyzed 24 water quality variables from March 2016 to February 2018, at 7 study sites, along a 2320-km river stretch. The data revealed large spatiotemporal variations in total dissolved solids, major ions, nutrients, dissolved organic carbon, biological oxygen demand (BOD), chemical oxygen demand, chlorophyll a biomass (Chl a) and gross primary productivity. Principal component analysis identified three major determinants (source input, stream flow, and tidal influence) explaining over 84% of the total variance. A high concentration of oxygen-demanding chemicals, especially in the middle segment, underscores the importance of restoration efforts that address BOD reduction alone. This work advances our understanding with respect to inter-segment variations and factors regulating Ganga River water quality and demonstrates the significance of watershed-scale studies for integrated river basin management.