The water quality has degraded with economic development globally. However, the relationship between food-web structure and nitrogen and phosphorus is of rare concern. To study food chain in this ecosystem, we measured the concentrations of stable isotope value δ¹³C and δ¹⁵N in aquatic matter and organisms in Pearl River. The δ¹³C and δ¹⁵N concentrations ranged from −41.2‰ to −19.4‰ and from 0.81‰ to 25.4‰, respectively. The δ¹³C concentrations in consumers were significantly higher than the particulate organic matter (POM), periphyton, phytoplankton, and higher aquatic plants. The δ¹³C of POM was likely derived from phytoplankton and exogenous organic detritus entering from a tributary, rather than from endogenous phytoplankton in the main river channel. The δ¹³C of phytoplankton was derived from eutrophic water with high nitrogen and phosphorus concentrations. Total δ¹³C was significantly higher in fish than in POM, phytoplankton, higher aquatic plants, and zooplankton, indicating that those components were the main carbon sources for fish. The carbon sources tended to be the same for different fish species in the same season at the same site, but different for a given fish species among seasons and sampling sites. This finding suggested that the feeding habits of different fish species converge as an adaptation to change environment. The food chain was longer (trophic level = 4.4) in river subsections with more carnivorous fish, such as Erythroculter pseudobrevicauda and Coilia grayii, and shorter in areas with more omnivorous fish. The total nitrogen and total phosphorus concentrations in the water were negatively correlated with food-chain length (R² = 0.67, P<0.05; R² = 0.40, P<0.05). These results suggested that limiting nitrogen and phosphorus inputs into the water body would reduce the ecological risk in this area.