Unidirectional water flow results in the downstream-biased, asymmetric dispersal of many riverine organisms. However, little is known of how asymmetric dispersal influences riverine population structure and dynamics, limiting our ability to properly manage riverine organisms. A metapopulation of the freshwater pearl mussel Margaritifera laevis may be sensitive to river currents because mussels are repeatedly exposed to downstream drift during floods—a parasitic life stage is the only, limited period (~40 days) during which larvae (glochidia) can move upstream with the aid of host fish. We hypothesized that water-mediated dispersal would overwhelm upstream dispersal via host fish, and therefore, that upstream subpopulations play a critical role as immigrant sources. To test this hypothesis, we examined the effects of both up- and downstream immigrant sources on the size of target subpopulations in the Shubuto River system, Hokkaido, Japan. We found that target subpopulation size was dependent on the upstream distribution range of reproductive subpopulations and the number of upstream tributaries, which are proxies for the number of potential immigrants moving downstream. In contrast, little influence was observed of downstream immigrant sources (proximity to downstream reproductive subpopulations). These results were consistent even after accounting for local environments and stream size. Our finding suggests that upstream subpopulations can be disproportionately important as immigrant sources when dispersal is strongly asymmetric.