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Biological carbon pumping (BCP) is a key process in which dissolved inorganic carbon in terrestrial aquatic ecosystems is utilized by aquatic autotrophs for photosynthesis and transformed into autochthonous organic matter (AOC). However, the mechanisms underlying BCP and the amount of generated AOC deposited effectively, are still poorly understood. Therefore, we conducted a systematic study combining modern hydrochemical monitoring and a sediment trap experiment in Fuxian Lake (Yunnan, SW China), the second-deepest plateau, oligotrophic freshwater lake in China. Temperature, pH, EC (electrical conductivity), DO (dissolved O2), [HCO3−], [Ca2+], SIc, partial CO2 (pCO2) pressure, and carbon isotopic compositions of HCO3− (δ13CDIC) in water from Fuxian Lake all displayed distinct seasonal and vertical variations. This was especially apparent in an inverse correlation between pCO2 and DO, indicating that variations of hydrochemistry in the lake water were mainly controlled by the metabolism of the aquatic phototrophs. Furthermore, the lowest C/N ratios and highest δ13Corg were recorded in the trap sediments. Analyses of the C/N ratio demonstrated that the proportions of AOC ranged from 30% to 100% of all OC, indicating that AOC was an important contributor to sedimentary organic matter (OC). It was calculated that the AOC flux in Fuxian Lake was 20.43 t C km−2 in 2017. Therefore, AOC produced by carbonate weathering and aquatic photosynthesis could potentially be a significant carbon sink and may have an important contribution to solving the lack of carbon sinks in the global carbon cycle. [ABSTRACT FROM AUTHOR]