We used variation in algal δ13C between river habitats to study the spatial scale of energy flow through river food webs. We found a strong negative relationship between herbivore δ13C (which reflects algal δ13C) and water velocity in three productive Northern California rivers but not in unproductive streams. The contrast among habitats suggests that water velocity affects algal δ13C most strongly when CO2 availability is low relative to photosynthetic rates. Our results help explain the wide variation in published river biota δ13C and show that past studies using carbon isotope analyses may have significantly underestimated the importance of algal-derived carbon to river food webs. While flow-related variation in δ13C complicates this common application of carbon isotope analysis, we show that it provides a natural tracer of the flux of algal production derived from different habitats within rivers to higher trophic levels. Measurements of consumer δ13C showed that most invertebrate and vertebrate consumers relied on local production, except for filter-feeding insects and steelhead trout, which relied on production derived from multiple sources. Stable carbon isotopes may thus be used to spatially delineate the habitats that support river food webs, providing previously unavailable information for understanding and managing river ecosystems.