ABSTRACTAim Waterbirds may play an important role in the maintenance of aquatic ecosystem biodiversity by transporting plants and invertebrate propagules between different wetlands. The aim of this study is to provide the first quantitative analysis of the transport of plant and animal propagules by a community of waterbirds.Location Doñana marshes in south‐west Spain.Methods 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 Doñana).Results 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.Main conclusions The abundance of different propagule types varied between waterfowl species in a seasonal and species specific manner, probably owing to differences in foraging strategies, bill and gut morphology, and seasonal shifts in propagule availability or distribution. Lamellar density was positively correlated with the abundance of intact propagules. Our results confirm that waterfowl play an important role in the dispersal of organisms in aquatic environments by internal transport. Wherever there is a propagule bank accessible to waterbirds, transport can occur even when propagule production and waterfowl movements do not overlap in time.