Closely linked with hydrological and biological processes, karst carbon cycle, involving the migration, transformation, and storage of inorganic carbon and organic carbon components within karst systems, responds rapidly to environmental changes. To cope with arid environments, plants in karst regions can utilize groundwater, but their impact on karst carbon cycling remains unclear. Further research is urgently needed to determine if plants can photosynthetically utilize groundwater HCO3- and how this process affects the karst carbon cycle. Based on hydrochemical and isotopic data from spring waters in the Mashan and Langshi regions of the Li River Basin in Southwest China during both rainy and dry seasons, this study elucidates the water-carbon coupling mechanisms in the karst critical zone under drought conditions. Key findings include: HCO3- in groundwater primarily originated from rock weathering, with carbonate weathering by carbonic acid accounting for 87.99% of total dissolved inorganic carbon. During the dry season, prolonged groundwater residence time resulted in intensified water-rock interactions. Significant enrichment of S13CDIC and S13CTOC of groundwater in the dry season, compared to the rainy season, indicates a shift in plant carbon sources from atmospheric CO2 to HCO3- in groundwater. This carbon source transition elevates S13C in plant tissues and soil organic carbon, while subsequent terrestrial organic carbon transport further modifies S13C values of inorganic and organic carbon in groundwater. These findings demonstrate that the karst dynamic system couples hydrological, lithological, pedological, biological, and atmospheric components, thereby underscoring the need for incorporating vegetation and hydrological processes in karst carbon cycle studies.