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Rio Grande water is intensively managed and regulated by international and interstate compacts, Native American treaties, local water rights, and federal, state, and local agencies. Legislation and engineering projects in the early twentieth century brought about water impoundment projects and channelization of the Rio Grande which led to the eventual loss of floodplain habitats. In particular, current water management practices in the Middle Rio Grande (MRG) have altered the natural flood regime altering the riparian community and floodplain dynamics which may be causing the demise of many fish species by altering food web processes. The Rio Grande silvery minnow (Hybognathus amarus), a federally endangered species, has been classified as an herbivore, detritivore, or carnivore. During low flow conditions H. amarus is primarily an algivore; however, during flood conditions, hydrodynamic scouring reduces or eliminates benthic algal food sources. The objective of this study was to identify and characterize food resources and trophic interactions for H. amarus on a restored floodplain during an extended flood-pulse release from reservoirs using stable isotope analyses (delta C-13 and delta N-15) and paleolimnology techniques. Results from stable isotope ratios indicate that H. amarus obtained carbon primarily from chironomids while aquatic invertebrates (including chironomids) obtained their carbon from macrophytes. Results from the GLIMMIX procedure indicate that the range of isotopic signatures for prey items was much broader at parallel habitats (i.e. floodplain flow parallel to main stem flow) than perpendicular (i.e. floodplain flow perpendicular to main stem flow) or leeward habitats (i.e. leeward sides of island where flow was near zero) indicating a wider selection of food resources. This study suggests that increased duration of floodplain inundation in the MRG provides vital habitats for spawning, nursery, and recruitment of threatened and endangered fish species. A combination of allochthonous and autochthonous resources best describes the nutrient and energy transfers for the Los Lunas, NM restored floodplain.