Summary Very little is known about the ecosystem impacts of river salinization despite expectations for global increases in salinization with growing water demand and climate change. In some rivers in the southwestern United States, salinization has occurred as a result of natural saline inputs exacerbated by flow alteration and other anthropogenic impacts. Salinization in the Pecos River has been linked to declines in fish diversity, but impacts on the structure of aquatic food webs have not been investigated. We assessed variation in local food webs along the longitudinal gradient of the main stem Pecos River by estimating carbon sources, trophic positions and assemblage‐wide trophic structure for aquatic consumers at 12 sites using stable isotope analysis (δ13C and δ15N). Temporal variation across seasons was also examined for common fish species at a subset of sites. Consumer richness, food‐chain length and assemblage‐wide niche breadth were inversely related to specific conductivity. Mixing models revealed differences in sources of dietary carbon supporting fish production along the longitudinal fluvial gradient, with a shift towards reliance on algal production in the salinized reaches of the river. Trophic niche breadth was greatest for assemblages in less degraded sites with higher fish species richness. Local food webs in salinized sites were dominated by euryhaline species and had shorter food chains and narrower assemblage‐wide niche breadths. Across seasons, δ13C and δ15N signatures remained fairly constant for five common fish species. Our results suggest that salinization in portions of the Pecos River constrains the diversity of consumers and trophic resources in local food webs. Characterising changes in food‐web structure in relation to salinization and other environmental changes is important for habitat assessment, stream restoration and other conservation strategies.