A metapopulation of the freshwater pearl mussel, Margaritifera laevis, may be influenced by the river currents because mussels become primarily passive dispersers as juveniles following a parasitic life stage, the limited period during which larvae (glochidia) can move upstream and tributaries with the aid of host fish. Based on extensive surveys for reproductive subpopulations and their sizes, we analyzed factors influencing subpopulation sizes of M. laevis in the Shubuto River system, Hokkaido, to infer its metapopulation dynamics. The subpopulation size was dependent on the upstream distribution range of reproductive subpopulations and the number of upstream tributaries, which are proxy variables for the amount of potential immigrants moving down the river, even after accounting for effects of stream size and local environments. Potential immigrants may include individuals reproduced or dislodged from upstream subpopulations. Our results suggest that asymmetric dispersal process can be a key to structuring riverine metapopulations.