The quantification of carbon cycling across the groundwater–stream–atmosphere continuum (GSAC) is crucial for understanding regional and global carbon cycling. However, this quantification remains challenging due to highly coupled carbon exchange and turnover in the GSAC. Here, we disentangled carbon cycling processes in a representative groundwater–stream–atmosphere transect by obtaining and numerically simulating high-resolution time series of dissolved He, Ar, Kr, O₂, CO₂, and CH₄ concentrations. The results revealed that groundwater contributed ∼60% of CO₂ and ∼30% of CH₄ inputs to the stream, supporting stream CO₂ and CH₄ emissions to the atmosphere. Furthermore, diurnal variations in stream metabolism (-0.6 to 0.6 mol O₂ m^-2 day^-1) induced pronounced carbonate precipitation during the day and dissolution at night. The significant diurnal variability of biogeochemical processes emphasizes the importance of high-resolution time series investigations of carbon dynamics. This study shows that dissolved gases are promising environmental tracers for discerning and quantifying carbon cycling across the GSAC with high spatiotemporal resolution. Our high-resolution carbon exchange and turnover quantification provides a process-oriented and mechanistic understanding of carbon cycling across the GSAC.