Human alteration of river ecosystems is an enormous concern worldwide. This study is focused in the Middle Rio Grande (MRG) of New Mexico, which has been severely altered since the early 1900s. The overall aim of the research is to document present conditions and reconstruct past conditions of the MRG aquatic food web to understand how river regulation (e.g., dam and levee construction, large-scale diversion of water for human use) has affected organisms that live there. Naturally occurring stable isotopes will be used as biochemical tracers to document production and cycling of food energy through the entire MRG ecosystem from plants to fishes. We will then compare isotope signatures of present day fishes to historical fish specimens held in the Museum of Southwestern Biology (up to 63 years) to evaluate (i) changes over time in carbon sources entering the food web due to altered flood cycles, (ii) changes in fish food web as non-native fish species increased in abundance and many native fishes declined, and (iii) variation in nitrogen fertilizer inputs from agriculture over time. This research will advance knowledge of how aquatic communities respond to river regulation over decadal time spans. More broadly, this research focuses on developing a novel method to address the challenging problem of reconstructing community food web structure and function following river ecosystem alteration.