To date, our ability to speculate how species interactions will change temporally and spatially in response to WLR still inadequate, especially within large river-reservoir ecosystems. Fish communities in backwater bay of the Xiaojiang River of the TGR (Three Gorges Reservoir) were studied in 2010 and 2016 using a stable isotope approach to explore variations in fish trophic niches associated WLR. We found that fish assemblages tended to have broader trophic diversity spaces in LBAs (large backwater areas) at a water depth of 175 m, suggesting that the assimilation of food resources might come from a greater diversity of habitats or prey items with distinct isotopic signatures. Many among-fish species trophic niches tended to overlap and have broader ranges in LBAs compared to SBAs (small backwater areas) at a water depth of 145 m, which indicated that the processes of impounding at 175 m can provide more similar food resources for different fish species. Our findings highlight that WLR dynamics are typical characteristics of the backwater bay of the Xiaojiang River aquatic ecosystems caused by the operations of the TGR, which has significant ecological effects on the fish trophic structure within this community. Understanding the pattern of changes in fish trophic niche associated with WLR will be meaningful for fishery resources management of the other tributaries in the TGR.