Atmospheric carbon sequestered in karst systems through dissolution of carbonate minerals is considered to have no net effect on long-term regional and global carbon budgets because precipitation of dissolved carbonate minerals emits CO 2 back to the atmosphere. Even though recent studies have implied that rapid kinetics of carbonate dissolution coupled with the aquatic photosynthetic uptake of dissolve inorganic carbon (DIC) could facilitate a stable atmospheric C sink in karst rivers and streams, little is known about the magnitudes and long-term stability of this C sink. To assess in-stream biogeochemical processes and their role on stream C cycling, we measured diel cycles of water characteristics and chemical composition (temperature, pH, DO, SpC, DIC, Ca 2 + , δ 13 C DIC ) in a groundwater-fed karst stream in southwest China. Our results show no diel variations at the groundwater discharge point (CK site) due to the absence of a sub-aquatic community (SAC). However, all hydrochemical parameters show significant diel cycle 1.3 km downstream (LY site). Diel variations in pH, DO, and δ 13 C DIC were inversely related to diel changes in SpC, DIC, Ca 2 + and p CO 2. This result indicates that in-stream metabolism (photosynthesis and respiration) of SAC controls diel variations in stream water chemistry. Significant diel cycles of net ecosystem production (NEP) influences in-stream diel fluctuation of pH, DO, SIc, DIC, p CO 2 , Ca 2 + and δ 13 C DIC, with gross primary production (GPP) dominating in day and ecosystem respiration (ER) dominating at the night. Absence of in-stream metabolism at CK enhances CO 2 degassing from stream to the atmosphere, which is estimated to be 3– 5 times higher than at LY. We estimate the carbon sink through in-stream metabolism of SAC to be 73 t C km − 2 a − 1 , which is around half the rate of the oceanic biological pump. These results imply in-stream photosynthesis sequesters DIC originating from karst weathering and controls CO 2 evasion. [ABSTRACT FROM AUTHOR]