Natural lakes are significant global sources of CO₂ emissions; however, data from lakes in karst regions, which cover 15.2 % of the Earth’s surface, remain insufficiently categorized. This study seeks to elucidate the carbon budget processes and drivers in karst lakes by selecting representative karst and non-karst lakes within the same region. Utilizing high-resolution monitoring, carbon isotope analysis, and mathematical modeling, we investigated the carbon source-sink functions and their controlling factors across different lithologies. Our findings reveal that metabolic processes, quantified using a bookkeeping model, are crucial for driving the diurnal coupling of hydrochemistry and carbon cycling, with karst lakes displaying a pronounced net autotrophic state. Carbon sink fluxes, determined via the boundary layer method, were estimated to be 38 t C km⁻² yr⁻¹ for the karst lake, and 11 t C km⁻² yr⁻¹ for the non-karst lake. This indicates that despite high dissolved inorganic carbon (DIC) concentrations, the metabolic processes in karst waters, facilitated by their high pH and efficient DIC fertilization, lead to a lower CO₂ emission. Furthermore, the low Revelle factor (3.8–4.8) highlights the strong carbonate buffering capacity of karst lakes against CO₂. These findings emphasize the capacity of karst lakes to maintain net autotrophy and function as carbon sinks, together with the need to consider lithological differences in future assessments of regional or global lake carbon budgets.