Large seasonal water-level fluctuations may influence isotopic signatures of primary producers and the types and amounts of these potential food sources accessible to aquatic fauna of Poyang Lake, the largest freshwater lake in China. In this study, the isotopic signatures of primary producers and consumers were determined, stable carbon and nitrogen isotope analysis and mixing models were combined to investigate the influence of water levels on the diet and isotopic composition of Poyang Lake fish and invertebrates. Five potential food sources (seston, benthic organic matter, aquatic macrophytes, attached algae, and terrestrial plants), 4 species of invertebrates, and 10 species of fish were collected from the lake area during dry and wet seasons between January 2009 and April 2010. The δ 13C values of invertebrates and most fish were within the range of δ 13C values of the potential food sources for both seasons. The δ 13C values of invertebrates and most fish were lower in the dry season than in the wet season, whereas the δ 15N values exhibited different patterns for different species. Mixing models indicated that the most important food sources for common lake fauna were seston in the dry season and aquatic macrophytes and terrestrial plants in the wet season. The fauna were more omnivorous in the wet season than in the dry season. The food web dynamics of Poyang Lake are strongly influenced by changes in the abundance and accessibility of different basal food sources that occur because of seasonal flood pulses. The trophic links within the aquatic communities of Poyang Lake are modified by water-level fluctuations.