Waterfowl often have been assumed to disperse freshwater aquatic organisms between isolated wetlands, but no one has analyzed the impact of this transport on the population structure of aquatic organisms. We quantified the number of intact seeds and invertebrate eggs in 386 faecal samples from 11 migratory waterfowl species (10 ducks and coot), collected from 3 November to 3 December 1998 (when birds were arriving from further north), and 22–25 February 1999 (when birds were leaving Doņana, Spain). Intact seeds of at least 7 plant genera, and invertebrate eggs (ephippia of at least 2 crustacea, statoblasts of at least 2 bryozoans and eggs of Corixidae) occurred in 65.6% of the faecal samples in early winter and 67.8% in late winter. We determined the impact of propagule transport on organisms population structure across using published sequences of several mitochondrial DNA genes and genotypic frequencies at allozyme and microsatellite loci. For three cladocerans (Daphnia ambigua, Daphnia laevis, and Sida crystallina) and one bryozoan (Cristatella mucedo), we estimated the genetic distances between populations across North America. Waterfowl movements across North America (estimated from band recovery data) explained a significant proportion of the gene flow occurring between populations across the continent for three of the four species, even after controlling for geographic distances between localities. The fourth species, S. crystallina, has propagules less likely to survive desiccation or ingestion by birds. Differences in the capacity to exploit bird-mediated transport are likely to have important consequences for the ecology of aquatic communities and the spread of invasive species.