Freshwater organisms remain at risk from bioaccumulation and biomagnification of persistent organic pollutants (POPs), but factors affecting their transfer through food webs are poorly understood. Here, we investigate transfer pathways of polychlorinated biphenyls, polybrominated diphenyl ethers, and organochlorine through a river food web, assessing the distribution and flux between basal resources (n = 3), macroinvertebrates (n = 22), and fish (n = 1). We investigate the effects of biological traits on the observed patterns and use trait-based models to predict POP bioaccumulation. Transfer pathways differed among POPs and traits such as habitat affinity, feeding behavior, and body size explained some variation in POP burdens between organisms. Trait-based models indicated that relationships between POPs, trophic transfers, and traits were relatively well conserved across a wider array of river food webs. Although providing more consistent predictions of POP bioaccumulation than steady-state models, variability in bioaccumulation across food webs limited the accuracy of trait-model predictions. As some of the first data to illustrate how ecological processes alter the flux of pollutants through river food webs, these results reveal important links between POPs and contrasting energetic pathways. These data also show the utility of trait-based methods in the assessment of persistent contaminants, but further field validations are required.