High-resolution hydrochemical data from five spring-fed ponds are presented to demonstrate the effect of different land uses and aquatic biological processes on the carbon cycle at a karst-analog test site. The results show that hydrochemical parameters including pH and the concentrations of HCO₃⁻, Ca^{2 +}, NO₃⁻, partial pressures of CO₂(pCO₂) and dissolved O₂ (DO) as well as carbon isotopic compositions (δ¹³C) of HCO₃^–in the pond water all displayed distinct diurnal variations, while those of the spring water itself were rather stable. The coupled dynamic behaviors of pCO₂, DO and NO₃⁻ indicate a significant influence from the metabolism of submerged plants in the ponds. In the afternoon, when photosynthesis is the strongest, the pCO₂ of the five pond waters was lower even than that of the ambient atmosphere, demonstrating the existence of a “biological carbon pumping (BCP) effect”, similar to that in the oceans. It was determined that, in October (autumn), the BCP fluxes in the five spring-fed ponds were 156 ± 51 t C km^{− 2} a^{− 1} in P1 (Pond 1 – adjoining a bare rock shore), 239 ± 83 t C km^{− 2} a^{− 1} in P2 (adjoining uncultivated soil), 414 ± 139 t C km^{− 2} a^{− 1} in P3 (adjoining land cultivated with corn), 493 ± 165 t C km^{− 2} a^{− 1} in P4 (adjoining grassland) and 399 ± 124 t C km^{− 2} a^{− 1} of P5 (adjoining brushland), indicating the potentially significant role of aquatic photosynthesis in stabilizing the carbonate weathering-related carbon sink. In addition, by comparing the DIC concentrations and fluxes of DIC transformed into autochthonous organic matter (AOC) in the five ponds, the so-called “DIC fertilization effect” was found in which more AOC is produced in pond waters with higher concentrations of DIC. This implies that the carbon cycle driven by aquatic biological processes can be regulated by changing land use and cover, the latter determining the DIC concentrations. Further, the rock weathering-related carbon sink is underestimated if one only considers the DIC component in surface waters instead of both DIC and AOC.