Stable isotope analysis was used to investigate the migratory status and to determine the relative contribution of allochthonous and autochthonous sources of carbon for the major riverine fish species (Barbus altianalis and Labeo victorianus) in rivers draining the Kenyan side of Lake Victoria. The two fish species derived carbon from both C4 and C3 plant sources, although L. victorianus exhibited less enriched isotopic carbon values. Fish samples from stations under direct influence of effluents from sugar factories exhibited enriched δ13C signals. Assuming that this reflects carbon sourcing from riparian C4 plants, it suggests that carbon from terrestrial sources can be a major energy source in some rivers. This heavy carbon enrichment associated with sugar factories was spatially restricted and occurred in all seasons, implying that sub-populations of the two fish species are non-migratory. The large migratory populations of these two species, for which Lake Victoria was once famous, may be no more.