A poor understanding of factors leading to species decline can result in inefficient or ineffective species restoration. Endangered Colorado Pikeminnow ( Ptychocheilus lucius) was nearly extirpated from the San Juan River, NM, USA and recent efforts to reestablish the species via hatchery augmentation of juveniles has yet to reach the targeted number of adults in the system. To assess how changes to the river’s food web could be limiting reestablishment of this top predator, we used stable isotope (δ ¹³C and δ ¹⁵N) signatures of the fish community pre- (museum specimens) and post river regulation with coincident extirpations and invasions. Following river regulation, four of five community-wide trophic structure metrics used to quantify resource use diversity were reduced and species turnover likely had little effect per se. For species sampled in both time periods, shared trophic resources generally increased (mean niche overlap = +35.7%). However, Colorado Pikeminnow experienced a large decrease in niche breadth (-72%) and diet mixing models suggested a shift from piscivory towards insectivory in contemporary collections. Our results suggested an overall reduction in basal resource availability after river regulation. We suggest increased reliance on similar resources may be limiting fish prey for Colorado Pikeminnow, ultimately contributing to the slow and limited reestablishment in the San Juan River. This study adds to the growing body of knowledge provided by museum specimens and stable isotope analyses to identify food-web dynamics that are a departure from historical conditions which can provide novel information critical to imperiled species management in modified systems.