In riparian ecosystems, river flow is the dominant driver influencing ecological process and pattern, including the recruitment of riparian tree species. In a four-year field study (1997–2000) of seedling recruitment on sandbars in the Wisconsin River, I evaluated the hypothesis that the timing of seed dispersal and river flow interact to determine the annual composition of pioneer tree seedling cohorts. In the final three years of the study (1998–2000), growing season flow pulses strongly influenced the species composition and density of new seedling cohorts. Mortality rates of new seedlings exceeded 90% during the 1998 and 1999 flow pulses, and species composition shifted to dominance by Acer saccharinum following the 1999 flow pulse. Different species dominated the cohort of each year: in 1997, 83% of new seedlings were Betula nigra; in 1998, 63% were Salix spp. (S. nigra 39%, S. exigua ssp. interior 24%); in 1999, 89% were Acer saccharinum; and in 2000, 71% were S. exigua and 23% were Betula nigra. Cohorts retained their initial differences in species composition for at least one year after establishment. The three years (1998–2000) with summer flow pulses produced very low end-of-the-growing-season densities of new seedlings (<0.1 seedlings/m² on random plots), and subsequent mortality in the first year after establishment further reduced seedling numbers by 53–94% on monitored plots. Thus, although summer flow patterns during the first year of growth strongly influenced species composition of seedling cohorts, low seedling densities and high overwinter mortality likely reduce the long-term impacts of initial cohort differences on successional trajectories.