Signatures of stable isotope ratios have previously been used to trace the source and transport of particulate organic matter (POM) in freshwater and marine ecosystems. In this study, water columns were collected at 22 sites in the littoral zone of Lake Taihu in 2014 to investigate the distribution and concentration of nutrients and the stable isotope signatures of POM, and their potential interrelation. Generally, mean concentration of nitrogen forms (NH4+-N) showed substantial variation, probably because they had received large amounts of wastewater from various local industrial enterprises. Source analysis by stable carbon and nitrogen isotopic ratios showed that the main POM sources were phytoplankton. Contrasting correlations were obtained between δ15N and N concentrations in effluent river mouths when compared with influent river mouths. In effluent river mouths, there was a significant positive correlation between δ15N and nitrogen concentration (total nitrogen and ammonia-nitrogen), in contrast with the negative correlation in influent river mouths. According to these results, more factors should be taken into consideration when stable carbon and nitrogen isotopes of POM are used to assess the feeding relationship between consumers and prey, as well as the energy flow pathways that support the lake pelagic food webs.