Abstract: According to the situation of severe non-point source pollution in agriculture, taking Nanjing Gaochun irrigation area as study area, the contributions of endogenesis and exogenous inputs to the system were invetigated using stable carbon and nitrogen isotope characteristics analysis. The results showed that the stable carbon and nitrogen characters of the particulate organic matter (POM) varied greatly, the average value was -27.82‰, closed to the aquatic plants and phytoplankton, which may be the main sources of POM. The main factor of phytoplankton was δ13C of DIC (dissolved inorganic carbon) in the water, the linear correlation between δ13C of DIC and δ13C of phytoplankton proved DIC concentration of the δ13C of phytoplankton. In this experiment, each sampling point between phytoplankton and POM was no significant difference, meanwhile the δ13C of zooplankton and phytoplankton were correlated, indicated that zooplankton concentrated organic carbon from phytoplankton as food. The δ13C value changed in sediment range between -27.2‰ to -21.8‰, more carbon than POM, which indicated that sediment composition accumulated more organic carbon than the water particles. The average of δ15N in this experiment was -0.6 ‰, closed to N2 in atmosphere.