The headwaters of the Ganga (the Alaknanda, Bhagirathi and the Ganga) were analysed for their dissolved major ions, Sr and 87Sr/86Sr on a biweekly to monthly basis over a period of one year to determine their temporal variations and the factors contributing to them. The concentrations of major ions and Sr show significant seasonal variation with lower values during monsoon period in all the three rivers. A similar trend is also observed for 87Sr/86Sr and Na*/Ca (Na* = NarClr) suggesting relatively lower contribution of Sr and Na from silicates (which are more radiogenic in Sr) during monsoon. Budget calculations show that silicate derived dissolved Sr (Srs) in the river Ganga, Alaknanda and the Bhagirathi varied from 10 ± 4 to 27 ± 11, 7 ± 3 to 30 ± 12, 16 ± 6 to 57 ± 23% of measured Sr respectively with lower values during monsoon. The relative decrease in silicate erosion compared to carbonate during monsoon can result from several factors, these include higher dissolution kinetics of the carbonates, lower water–rock interaction time and availability of larger area for weathering. The annual discharge weighted Sr flux derived from the time series data is higher by ∼20% from that based on peak flow Sr, and lower by ∼40% compared to that derived from lean flow Sr concentration. The area-normalized annual flux of dissolved Sr from the Ganga at Rishikesh is about five times its flux at Rajshahi (Bangladesh) and a few other major global rivers, such as the Amazon, indicating higher erosion rate over the Himalaya.