Abstract: In this study, we investigated the food web and the trophic relationships in the Gonghu Bay of the Taihu Lake by using the stable carbon and nitrogen isotopes. The present study showed that the structure of the food web and the trophic interaction were complex in the shallow lakes due to changes in the material sources, the bio-food sources and other factors. We found that omnivores were common species in the aquatic ecosystems. The complexity in the carbon sources and the bio-interactions was a limiting factor in the evaluation of the network in the aquatic ecosystems. Nevertheless, we still discovered that the major sources for the food web of the Gonghu Bay were phytoplankton, benthic algae, and macrophytes, and that the terrestrial sources of carbon only made a small contributed to the food web. We also observed some differences in the ratios of 15N and 13C among the major organisms in the Gonghu Bay. The 13C values of the consumers ranged from -32.3 (Chironomus sp.) to -22.1 (Neocaridina denticulata sinensis), and the consumers at higher trophic levels had lager 15N values. The lowest 15N value was 10.3 (Cristaria plcata), and the highest was 19.0 (Hyporhamphus intermedius). There was no correlation between the ratios of 13C and the trophic relationships, neither between the ratios of 13C and 15N (r=0.1835, P 0.05), which suggested that the food web had a nonlinear structure. The length of the food chain in the Gonghu Bay was 4.44 trophic level.