Many aquatic and riparian plant species are characterized by the ability to reproduce both sexually and asexually. Yet, little is known about how spatial variation in sexual and asexual reproduction affects the genotypic diversity within populations of aquatic and riparian plants. We used six polymorphic microsatellites to examine the genetic diversity within and differentiation among 17 populations (606 individuals) of Sparganium emersum, in two Dutch-German rivers. Our study revealed a striking difference between rivers in the mode of reproduction (sexual vs. asexual) within S. emersum populations. The mode of reproduction was strongly related to locally reigning hydrodynamic conditions. Sexually reproducing populations exhibited a greater number of multilocus genotypes compared to asexual populations. The regional population structure suggested higher levels of gene flow among sexually reproducing populations compared to clonal populations. Gene flow was mainly mediated via hydrochoric dispersal of generative propagules (seeds), impeding genetic differentiation among populations even over river distances up to 50 km. Although evidence for hydrochoric dispersal of vegetative propagules (clonal plant fragments) was found, this mechanism appeared to be relatively less important. Bayesian-based assignment procedures revealed a number of immigrants, originating from outside our study area, suggesting intercatchment plant dispersal, possibly the result of waterfowl-mediated seed dispersal. This study demonstrates how variation in local environmental conditions in river systems, resulting in shifting balances of sexual vs. asexual reproduction within populations, will affect the genotypic diversity within populations. This study furthermore cautions against generalizations about dispersal of riparian plant species in river systems.

1. The potential for seed dispersal by fish (ichthyochory) will vary among aquatic plants because of differences in seed size and morphology. 2. To examine how seed morphology influences the probability of dispersal by the common carp (Cyprinus carpio), we studied seed ingestion, retention time and subsequent egestion and germination of seeds of Sparganium emersum and Sagittaria sagittifolia, two aquatic plant species with similar sized but morphologically different seeds. 3. We compared dispersal probabilities between the two plant species, in which the probability of dispersal is assumed to be a function of the probabilities of seed ingestion, egestion and germination, and the dispersal distance is assumed to be a function of seed egestion rate over time. 4. We found that, although the soft seeds of S. sagittifolia had an approximately 1.5 times higher probability of being ingested by the carp than the hard seeds of S. emersum (83.15% ± 1.8% versus 56.16% ± 2.7%, respectively), the latter had an almost twofold higher probability of surviving the passage through the digestive tract (38.58% ± 2.7% versus 20.97% ± 1.5%, respectively). Patterns of seed egestion over time did not differ between the two plant species, despite the difference in seed morphology. Gut passage had a different effect on seed germination between plant species. Compared with non-ingested controls, seeds of S. emersum showed a 12.6% increase in germination and a 2.1 day acceleration in germination rate, whereas seeds of S. sagittifolia displayed a 47.3% decrease and 5.1 day delay, respectively. 5. Our results suggest that seed morphology affects the dispersal probability and postdispersal establishment, but not the dispersal distance, of aquatic plants that are dispersed by fish.