Trophic linkages in Glen and Grand Canyons of the lower Colorado River downstream from Glen Canyon Dam were examined using multiple stable isotope analysis. The δ <sup>13</sup>C values of dissolved inorganic carbon (DIC), and the δ <sup>13</sup>C, δ <sup>15</sup>N, and δ <sup>34</sup>S values of seston, aquatic and terrestrial plants, and aquatic animals were determined. The δ <sup>13</sup>C value of DIC varied among sites. DIC from the epilimnion of the reservoir (Lake Powell) and from a tributary was more <sup>13</sup>C-enriched than DIC in the Colorado River, probably as a result of variation in aquatic primary production and dissolution of carbonate among sites. Four potential bases of aquatic secondary production: upland vegetation, riparian vegetation, reservoir plankton, and benthic algae were isotopically (δ <sup>13</sup>C and δ <sup>15</sup>N) distinct from each other. Analysis of δ <sup>13</sup>C, δ <sup>15</sup>N, and δ <sup>34</sup>S showed that seston from the dam tailwater (Glen Canyon) consisted of lotic algae and zooplankton from Lake Powell, except for the ultra fine fraction (<0.053 mm) which was derived from Lake Powell particulate organic matter. Longitudinal variation in the composition of Glen Canyon seston was generally small. Seston from a tributary (the Paria River) was derived from a mixture of upland and riparian vegetation and was isotopically distinct from Colorado River seston. Isotope analysis revealed three trophic levels in Glen Canyon: algae (Cladophora glomerata and diatoms), macroinvertebrates (e.g., Gammarus lacustris and chironomids), and fish (primarily rainbow trout, Oncorhynchus mykiss). Trout also consumed zooplankton exported from Lake Powell. Direct assimilation of algal N by trout was not indicated despite the high incidence of algae in trout stomachs. Isotope values of fishes (trout and speckled dace, Rhinichthys osculus) from Grand Canyon tributaries reflected variation in the trophic basis of fish production; one tributary fish population appeared to be supported by tributary autochthonous production or mainstem organic matter sources, and others were linked to riparian or upland organic matter inputs.