Seed dispersal in aquatic habitats is often considered to be a complex multistage process, where initial seed shadows are redistributed by water (hydrochory). The roles of hydrochory in seed dispersal and influencing population genetic structure were examined in Helmholtzia glaberrima using both ecological and genetic techniques. Ecological experiments showed that water can redistribute seeds and seedlings over local scales and that hydrochory can provide the potential for very long distance seed and seedling dispersal. Patterns of seedling genetic structure were affected by micro-drainages that direct water flow within populations and influence water-borne seed dispersal on a local scale. Strong non-equilibrium dynamics and persistent founder effects were responsible for the patterns of genetic structure observed among established populations of H. glaberrima. Classical metapopulation models best described dispersal patterns, while water-borne seed dispersal could potentially explain patterns of genetic differentiation within a stream system, it could not explain the distribution of genetic variation among stream systems. The current study found that although hydrochory influenced seed dispersal and seedling genetic structure within a population, it had little effect on the spatial pattern of genetic variation among established populations of H. glaberrima. Moreover, even though prolonged buoyancy and viability in water provide the potential for long-distance hydrochory, results presented here do not support the hypothesis that flowing water is an effective long distance seed dispersal vector for H. glaberrima. Taken together, these results suggest that the relative importance of gene flow via water-born seed dispersal in H. glaberrima may be low compared with that of some other riparian species.