The sources and transformation mechanisms of $\mathrm{HCO}_{3}^{-}$ in outlet water bodies of typical karst watersheds are crucial for conducting karst carbon sink accounting and assessing carbon sequestration capacity. Taking the Yaji Experimental Field in Guilin, Guangxi as the research subject, an earth system science perspective was adopted, combining high-resolution monitoring with monthly sampling techniques. Continuous measurements temperature, electrical conductivity (EC), and CO₂ were conducted at soil depths of 10 cm, 40 cm, and 90 cm. Simultaneously, soil water, air, and spring water samples were collected for the analysis of pH, CO₂, δ¹³C_DIC, $\mathrm{HCO}_{3}^{-}$, and other hydrochemical parameters. By coupling mathematical models with hydrogeochemical techniques, data-driven linear mixing models and hydrochemical was utilized to systematically analysis and interpret the sources, influencing factors, and migration characteristics of $\mathrm{HCO}_{3}^{-}$ within the soil-groundwater system. The proportion of $\mathrm{HCO}_{3}^{-}$ derived from soil CO₂ was found to be 80.00% in soil water and 70.06% at the karst spring outlet (S31), indicating that soil CO₂ is the dominant source of $\mathrm{HCO}_{3}^{-}$ in the soil-groundwater system. Soil CO₂ levels were primarily influenced by meteorological conditions, soil temperature, soil EC, and biological activity. During the rainy season, increased soil CO₂ and enhanced karst dissolution resulted in simultaneous rises in Ca²⁺ and $\mathrm{HCO}_{3}^{-}$ concentrations in S31. Based on the hydrochemical facies, calcite saturation index, and CO₂ degassing characteristics, it was found that the $\mathrm{CO}_{2}-\mathrm{HCO}_{3}^{-}-\mathrm{CaCO}_{3}$ system in the soil-groundwater continuum reaches a dynamic equilibrium. Overall, the dynamics of $\mathrm{HCO}_{3}^{-}$ in the karst small-watershed soil-groundwater system are governed by the coupled processes of “soil CO₂ generation, water-rock reaction, and hydrological transport”. This system exhibits a migration-transformation pattern characterized by “rapid generation in upper layers, enrichment in the middle layers, and stable output at the spring outlet”. Moreover, reprecipitation at the karst spring outlet acts as a mechanism for reducing $\mathrm{HCO}_{3}^{-}$ concentrations. The results are expected to provide scientific guidance for quantifying karst carbon sink fluxes and assessing carbon sequestration potential.