Carbon migration, transformation, and emissions as CO 2 in reservoir and lake systems have been extensively studied. However, uncertainties persist regarding carbon cycling variations in both karst and non-karst regions within large thermal stratified river-reservoir systems. To address this knowledge gap, we combined measurements of water chemistry, isotopic compositions (δ 13 C), partial pressure of CO 2 (pCO 2 ), and CO 2 fluxes (F CO2 ) to elucidate the differences, control mechanisms, and environmental effects of various carbon biogeochemical processes in the Hongjiadu reservoir (HJD, karst reservoir) and Shangyoujiang reservoir (SYJ, non-karst reservoir), Yangtze River basin, China. Our results demonstrate that key biogeochemical processes are associated with CO 2 production and emissions. The stronger biological carbon pump (BCP) effect in the lentic area of the HJD reservoir limited CO 2 emission (0.9 ± 5.0 mmol m -2 d -1 ) compared to the SYJ reservoir (50.9 ± 33.4 mmol m -2 d -1 ), leading to low dissolved inorganic carbon (DIC) and high saturation state of carbonate minerals in the lentic epilimnion. Although the released water from both reservoirs acted as hotspots for CO 2 emissions, the results of higher Revelle factor (RF) in the HJD reservoir than SYJ reservoir suggest the greater buffer capacity and lower sensitivity of OC degradation changes in DIC. Despite the shorter hydraulic retention time (HRT) of SYJ reservoir (120 d) compared to HJD reservoir (368 d), F CO2 was 3.5 times higher than that of the HJD reservoir (652.9 mmol m -2 d -1 ). Moreover, upon analyzing selected reservoirs worldwide, it becomes apparent that karst reservoirs demonstrate a reduced potential for CO 2 emissions. Our results indicate that the impact of varying geologic settings should be considered to minimize errors in regional and global CO 2 emission estimates.