Carbon sink research constitutes a significant topic in the study of the global carbon cycle. Recently, carbon sinks from terrestrial aquatic ecosystems, known as missing carbon, have been attracting increased attention. Since recent studies have found that carbonate-weathering-related carbon sinks comprise 94% of rock-weathering-related carbon sinks, carbon sinks in karst surface aquatic ecosystems play a particularly important role. In addition, the biological carbon pump effect, as a carbon stability and sequestration process, functions as an essential mechanism for the formation of long-term carbonate-weathering-related carbon sinks and a critical part of the carbon cycle. Carbon forms the core of the biological carbon pump, which plays a central role in the karst surface aquatic system, which is replete with dissolved inorganic carbon (DIC). At present, research into the biological carbon pump mainly focuses on two aspects: (1) the distinction between autochthonous and allochthonous sources for CO2 sinks, which is crucial for accurate evaluation and calculation of carbon sequestration of the biological carbon pump. These methods, including elemental ratio analysis (C/N ratios), single isotope composition, natural 14C and 13C isotopes and biomarker methods, have been utilized to distinguish the OC sources in aquatic ecosystems. Natural 14C and 13C isotopes composition and biomarker methods have great development prospects because of good stability and accuracy; and (2) the biological carbon pump effect on water environment indicators and water quality. In this paper, the differences between biological carbon pump and eutrophication, biological carbon pump effect on phosphorus removal and the influence of elemental-coupling relationship on biological species were discussed, which provided further evidence for studying biological carbon pump effect on water environmental improvement. In the future, the amount of carbon sinks of terrestrial aquatic ecosystems should be accurately estimated, and the effects of different climates and land use on carbon sinks should be determined precisely. In addition, it is necessary to elucidate the interaction mechanism between the biological carbon pump effect and the water environment. Important study topics include: (1) the validity of the “element ratio control hypothesis” regarding the surface aquatic ecosystem(the underlying reasons causing the different biological species in surface aquatic ecosystems are the different elemental-coupling stoichiometric ratios and the differences in biological species further explain the water quality); (2) the regulation of the biological carbon pump effect on the stoichiometric ratio; (3) the root causes of the formation of different carbon sink mechanisms (biological carbon pump effects and eutrophication); (4) the possible mechanism of the biological carbon pump effect on water environmental improvement through physical-chemical- bio-coupling, such as colloidal effects and adsorption coprecipitation. Finally, the possibility of applying the microbial carbon pump effect to terrestrial aquatic ecosystems was discussed.