These data were compiled for a manuscript that examines the riverine food-web structure of the Colorado River below Glen Canyon dam to its confluence with Lake Mead. Tissue from primary producers (vascular plants and algae) and consumers (aquatic invertebrates and fish) were collected before and after monsoon floods in 2006 along the 388 kilometer segment of the Colorado River in the Southwest US. Tissue samples were dried, ground, and analyzed for δ13C, δ15N, and δ2H stable isotope signatures and percent carbon and nitrogen. Analysis of these data focused on determining the proportion of terrestrial (allochthonous) vs. aquatic (autochthonous) organic matter sources at the base of the food web, trophic diversity of primary and secondary consumers, and food-chain in response to pulsed flows resulting from monsoon floods that rapidly increase streamflow and flush terrestrial detritus into the river.