In regulated freshwater ecosystems, the deposition process of organic carbon (OC) in sediment could be affected by all the changes of physical, chemical, and biological factors. To assess different hydrodynamic conditions on the deposition of OC in sediment, the combination of elemental and stable isotope analyses was carried out in two reservoirs: the Huairou Reservoir (HR), which undergoes seasonal water level fluctuation (WLF) like natural lakes, and the Shisanling Reservoir (SR), which undergoes daily WLF for the operation of pumped storage power station. In general, OC concentration and its variation were comparable in the two reservoirs, whereas the OC distribution showed completely different features. The OC burial rate in SR was nearly two times more than in the HR, which reflect the impact of WLFs on the erosion of soil. For the relative contribution of phytoplankton-derived OC (P-OC), macrophyte-derived OC (M-OC), and terrestrial OC (T-OC) in sediment, the T-OC and M-OC in the SR were both higher than those of the HR, whereas the P-OC was markedly lower. Furthermore, the classification of nearshore and offshore sediments suggested that hydrodynamic conditions affected the T-OC import by physical processes and the in situ contributions of P-OC and M-OC with a spatial difference. [ABSTRACT FROM AUTHOR]