The impounding process on natural rivers can alter the depositional storage of organic carbon. In this study, the terrestrial organic carbon in the sediment cores in two large deep-water reservoirs (Silin and Pengshui reservoirs) located in the lower reaches of the Wujiang River in the karst landscape of southwest China were used to be analyzed and quantified, by using lignin biomarker technology. The lignin in the sediment cores was mainly derived from the herbaceous tissues of the angiosperms, and the lignin was degraded by demethylation, demethoxylation and oxidative degradation of the side chains by white rot and brown rot bacteria. The end-member model showed that the contribution of exogenous organic carbon to the sediment core was slightly larger than that of endogenous organic carbon, with soil organic carbon contributing the most. The influence of river cascade damming on sedimentary organic carbon is manifested in the interception of exogenous organic carbon and the accumulation of endogenous organic carbon, and there is obvious spatial heterogeneity in the distribution of exogenous and endogenous organic carbon.