Since the stable isotope composition was widely used as tracers in the process of pollutant migration and transformation, stable isotope analyses of carbon and nitrogen in paddy field sampled from Nanjing irrigation area were studied. The results showed that delta C13 values of particulate organic matter (POM) were between -31.5‰～-24.3‰, with an average value of -27.7‰. The stable carbon and nitrogen characters of particulate organic matter (POM) varied greatly in different sites. The isotopic signatures of both POM and zooplankton remained sufficiently distinct from each other throughout the period of study. Delta C13 values of particulate organic matter and zooplankton showed some seasonal variation, reflecting higher values during spring and summer than autumn and winter. But delta N15 values were more constant except the last sampling. The spatial and temporal variations of delta C13 values were similar between zooplankton and POM, which meaned that POM may be the main resource of zooplankton. The minimum delta N15 value of POM was 3.1‰ and nitrogen fixation could be ignored in the study area. This study was the first to quantify such a seasonal switch in zooplankton and particulate organic matter in paddy field.