1. River systems offer special environments for the dispersal of aquatic plants because of the unidirectional (downstream) flow and linear arrangement of suitable habitats. 2. To examine the effect of this flow on microevolutionary processes in the unbranched bur-reed (Sparganium emersum) we studied the genetic variation within and among nine (sub)populations along a 103 km stretch of the Niers River (Germany-The Netherlands), using amplified fragment length polymorphisms. 3. Genetic diversity in S. emersum populations increased significantly downstream, suggesting an effect of flow on the pattern of intrapopulation genetic diversity. 4. Gene flow in the Niers River is asymmetrically bidirectional, with gene flow being approximately 3.5 times higher in a downstream direction. The observed asymmetry is probably caused by frequent hydrochoric dispersal towards downstream locations on the one hand, and sporadic zoochoric dispersal in an upstream direction on the other. The spread of vegetative propagules (leaf and stem fragments) is probably not an important mode of dispersal for S. emersum, suggesting that gene flow is mainly via seed dispersal. Realized dispersal distances exceeded 60 km, revealing a potential for long-distance dispersal in S. emersum. 5. There was no correlation between geographical and genetic distances among the nine S. emersum populations (i.e. no isolation by distance), which may be due to the occurrence of long-distance dispersal and ⁄ or colonization and extinction dynamics in the Niers River. 6. Overall, the genetic population structure and regional dispersal patterns of S. emersum in the Niers River are best explained by a linear metapopulation model. Our study shows that flow can exert a strong influence on population genetic processes of plants inhabiting stream systems.