The river–lake ecotone supports diverse aquatic life, but its food web structure and topology are poorly understood. Baiyangdian Lake, northern China’s largest shallow lake, depends on external environmental flows, of which the Fu River provides the most stable water supply. Here, we used stable isotopes and topological analysis to explore the food web structure along a spatial gradient using data from field surveys from 2018 to 2019. Carbon and nitrogen stable isotopes and the food web structure were associated with environmental factors for four ecosystem types (river, river mouth, lake mouth, lake). Detritus, phytoplankton, and zooplankton δ13C values became more depleted along the gradient from the river to the lake, whereas δ13C of submerged macrophytes was enriched in the ecotones compared to the river and lake. Higher δ15N values for basal resources and zooplankton occurred at the lake mouth and river mouth. The top consumers were omnivorous fish: Hemiculter leucisculus (trophic level [TL] = 3.85 ± 0.89) in the river and Pseudorasbora parva (TL = 4.54 ± 0.58) in the river mouth. Carnivorous Erythroculter dabryi occupied the highest TL (3.61 ± 0.36 and 4.46 ± 0.36, respectively) in the lake mouth and lake. These results together led to a change from a detritus-based to phytoplankton-based food web along the gradient from the river to the lake. The species richness, number of trophic links, link density, and mean food chain length all are greatest in the lake, followed by the lake mouth, and the lowest were in the river. Our results provide a holistic view of the ecotone ecosystem and its food web, suggesting that it supports a more diverse species assemblage and more complex food web structure than the adjacent river ecosystem, rather than the adjacent lake ecosystem. Therefore, management should emphasize the combined effects of altered hydrological regimes and poor water quality on the ecotone food webs to manage the river and lake more sustainably.