Nitrogen stable isotope composition (δ15N) of particulate organic matter (POM) has been used to infer dominant nitrogen cycling processes in lakes. However, very few studies have compared the isotope variations in lakes along trophic state and other biogeochemical gradients. Here we report an analysis of δ15NPOM and selected environmental variables from 96 subtropical lakes to assess the patterns and controls of isotope variations. Results indicate that δ15NPOM values varied from −2.8 to 13.2‰ and were not significantly correlated with total phosphorus (TP), total nitrogen (TN) and chlorophyll a (Chl a). The 15N depletion in POM was found across the entire trophic gradient and likely reflected contributions from planktonic nitrogen fixation. The 15N enrichment was attributed to high primary production and the contributions of anthropogenic wastes in eutrophic lakes, and the presence of microzooplankton in the water samples of the oligotrophic lakes. The δ15NPOM was negatively correlated with water color and positively correlated with pH. Because water color is indicative of light availability which affects phytoplankton growth and pH is significantly correlated with Chl a concentration in the study lakes, the close relationship between water color, pH and δ15NPOM therefore suggests primary productivity-driven isotope fractionation. Results from this study did not reveal the importance of trophic state, nitrogen concentration and surface area to the variations of δ15NPOM and points to the complex interactions of nitrogen cycling processes in lakes with diverse biogeochemical features.