It has long been presumed that waterbirds disperse the propagules of aquatic organisms. However, it is only in recent years that this claim has been empirically explored and little is still known about waterbird-mediated dispersal in southern Africa. Aquatic invertebrates are thought to be well adapted to dispersal by waterbirds because of their ability to produce hardy resting eggs. We explored the capacity of waterbirds to disperse the eggs of both cladocera and bryozoans via endo- and ectozoochory. We examined 283 faecal samples and 394 feather brushings from six waterbird species and two wetland sites in South Africa for the presence of diapausing eggs. A total of 108 intact diaspores were recovered, with intact eggs present in 16% and 7% of the faecal samples and feather brushings, respectively. Our results indicate that southern African waterbirds do take up the resting eggs of aquatic invertebrates and that these eggs can survive intact through the gut or remain attached to the feathers. These results provide evidence that waterbirds may be important vectors for aquatic invertebrates in southern Africa and imply that waterbirds may play a vital role in maintaining connectivity between invertebrate populations in isolated wetland patches.