Dams disrupt transport of organic matter and inorganic sediment from upstream, which can increase light transmission and the relative role of primary production to river carbon budgets. Glen Canyon Dam on the Colorado River has reduced sediment transport by 93%, and also organic matter input by an unknown amount. To quantify autochthonous inputs we measured primary production seasonally in the clear tailwater reach and at five sites within the Grand Canyon using a modified one-station open-channel metabolism method. In the tailwater reach primary production was always high, > 10 g O₂ m^-2 d^-1, and the reach was net autotrophic. Downstream within the Grand Canyon, gross primary production ranged from 4 g O₂ m^-2 d^-1 during clear water conditions to nearly zero during turbid conditions. In downstream reaches, episodic flooding of tributaries contributes substantially more carbon than inputs from primary production. While system-wide allochthonous inputs are high relative to autochthonous inputs, these inputs are spatially distinct. As a result, we predict that upstream food webs are supported by autochthonous carbon and downstream food webs are supported by a combination of both autochthonous and allochthonous carbon.