About two hydrological years of continuous data of discharge, temperature, electrical conductivity and pH have been recorded at the Glarey spring in the Tsanfleuron glaciated karst area in the Swiss Alps, to understand how glaciated karst aquifer systems respond hydrochemically to diurnal and seasonal recharge variations, and how calcite dissolution by glacial meltwater contributes to the atmospheric CO₂ sink. A thermodynamic model was used to link the continuous data to monthly water quality data allowing the calculation of CO₂ partial pressures and calcite saturation indexes. The results show diurnal and seasonal hydrochemical variations controlled chiefly by air temperature, the latter influencing karst aquifer recharge by ice and snowmelt. Karst process-related atmospheric CO₂ sinks were more than four times higher in the melting season than those in the freezing season. This finding has implication for understanding the atmospheric CO₂ sink in glaciated carbonate rock terrains: the carbon sink will increase with increasing runoff caused by global warming, i.e., carbonate weathering provides a negative feedback for anthropogenic CO₂ release. However, this is a transient regulation effect that is most efficient when glacial meltwater production is highest, which in turn depends on the future climatic evolution.