This study was undertaken in the Banzhai, a small groundwater-fed stream flowing over carbonate karst terrain in the southwest of Guizhou, China. To assess the biogeochemical processes behind carbon fluxes and sinks and calculate the end-member contribution to the geological carbon sink, samples were collected at a 2-h sampling interval during a two-day period, and the diel-variation of δ13CDIC, δ13CPOC, and C/N were analyzed. During the sampling period, temperature, pH, electrical conductivity (EC), dissolved oxygen (Do), and chlorophyll were measured at a 15-min interval using in situ sensors. The results showed that (1) the hydro-chemical variations reflected the photosynthesis of subaquatic plants and degassing. These processes likely turned a part of HCO3- to organic carbon, which subsequently precipitated. (2) The 13C isotope ratios indicated a varying intensity of photosynthesis and degassing during the HCO3- migration process. Moreover, subaquatic plants changed their metabolic pathway from C3 to C4 carbon fixation due to the lack of CO2 in the water and utilized HCO3- in the water as their carbon source. (3) The net carbon sink flux was 1784.54 kg CO2, where carbonate weathering, the biological carbon pump, and weathering of silicate rocks accounted for 85.80 %, 13.64 %, and 0.56 %, respectively. (4) In the Banzhai ground river, the DIC during the migration process was mainly lost through degassing, allogenic acid, and consumption by photosynthesis of subaquatic plants.