The biological carbon pump (BCP) associated with aquatic photosynthesis in karst surface waters converts dissolved inorganic carbon (DIC) into organic carbon. In the context of global climate change, BCP could be an important carbon sink mechanism, ultimately regulating atmospheric carbon dioxide (CO₂) and mitigating climate change. Because of the high DIC and pH, and low dissolved CO₂ [CO₂ (aq)], the hydrochemical characteristics of karst surface water bodies cause C limitation in BCP efficiency. The effect of CO₂ fertilization on water bodies can promote autochthonous production, thereby creating carbon sinks in such water bodies. The significant sink-enhancement potential of BCP in karst surface water bodies has attracted widespread attention. The stability of the autochthonous organic carbon (AOC) produced by BCP in karst aquatic ecosystems is key to the formation of long-term carbon sinks by carbonate weathering. In this review, we summarize recent progress in the carbonate weathering of carbon sinks in karst surface waters with coupled BCPs. Furthermore, we elucidated the possibility of using CO₂ (aq) fertilization to achieve carbon sinks and its mechanism of action. On this basis, we propose three processes and mechanisms that could affect AOC stability and outline the challenge of accurately estimating carbonate weathering carbon sinks associated with BCP in karst surface waters. Our comprehensive analyses facilitated the identification of the role of karst surface aquatic ecosystems in the global carbon cycle by providing a reference and scientific basis.