This study considered solute fluxes and the transient CO2 drawdown process in the highly glacierized Koxkar basin in Central Eurasia, around 70.20% of which is covered by present-day ice. From 27 June to 30 September 2011, the total runoff depth was 671.70 mm, which yielded crustal solute fluxes of 213.65 ± 10.05 kg·(km2·d)−1 that accounted for 53.59% of the total solute flux of the river water. The solute fluxes derived directly from ice meltwater and precipitation were 70.02 ± 4.68 and 16.57 ± 1.13 kg·(km2·d)−1, respectively, which accounted for 17.57% and 4.16% of the total solute flux. The carbonation and hydrolysis of carbonate and feldspar minerals occurred because of the presence of H+, supplied by sulfide oxidation or CO2 drawdown. While the H+ yielded by sulfide oxidation was insufficient for hydrochemical reactions, atmospheric CO2 dissolved in the water generated H+ that drove follow-up reactions. The total transient drawdown of CO2 was 804.83 t C, which generated 39.61% of the total HCO3- and 24.68% of the river water solute. Transient drawdown of CO2 in the glacier region indicated that change of glacial area and volume could influence atmospheric CO2 concentration and be important in the long-term global CO2 cycle.