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Natural and anthropogenic disturbances commonly alter patterns of biodiversity and ecosystem functioning. However, how networks of interacting species respond to these changes remains poorly understood. We described aquatic food webs using invertebrate and fish community composition, functional traits and stable isotopes from twelve agricultural streams along a landscape disturbance gradient.We predicted that excessive deposition of fine inorganic sediment (sedimentation) associated with agricultural activities would negatively influence aquatic trophic diversity (e.g. reduced vertical and horizontal trophic niche breadths). We hypothesized that multiple mechanisms might cause trophic niche ‘compression’, as indicated by changes in realized trophic roles.Food-web properties based on consumer stable isotope data (δ13C and δ15N) showed that increasing sediment disturbance was associated with reduced trophic diversity. In particular, the aquatic invertebrate community occupied a smaller area in isotopic niche space along the sedimentation gradient that was best explained by a narrowing of the invertebrate community δ13C range.Decreased niche partitioning, driven by increasing habitat homogeneity, environmental filtering and resource scarcity all seemingly lead to greater trophic equivalency caused by the collapse of the autochthonous food-web channel. Bayesian mixing-model analyses supported this contention with invertebrate consumers increasingly reliant on detritus along the sedimentation gradient, and predatory invertebrates relying more on the prey using these basal resources.The narrowing of the fish community δ13C range along the sedimentation gradient contributed to an apparent ‘trophic shift’ towards terrestrial carbon, further indicating the loss of the autochthonous food-web channel. On the vertical trophic niche axis, fish became increasingly separated from aquatic invertebrates with an increase in their estimated trophic position. In combination, these responses were most likely mediated through reduced fish densities and a diminished reliance on aquatic prey.Although species losses remain a major threat to ecosystem integrity, the functional roles of biota that persist dictate how food webs and ecosystem functioning respond to environmental change. Sedimentation was associated with nonlinear reductions in trophic diversity which could affect the functioning and stability of aquatic ecosystems. Our study helps explain how multiple mechanisms may radically reshape food-web properties in response to this type of disturbance.