The increased incidence of severe hypoxic ‘blackwater’ (high dissolved organic carbon, DOC) events as a consequence of river regulation and other river management practices poses a threat to the management of many river-floodplain systems. However, there is still a lack of fundamental knowledge regarding the effects of hypoxic blackwater events on the aquatic biota. Zooplankton occupy a central position in river-floodplain food webs, as consumers of algae, fungi and bacteria, and as potential prey items for fish, waterbirds, amphibians and macroinvertebrates. We investigated the impact of hypoxic blackwater events on river-floodplain zooplankton assemblages by examining the effects of varying DOC and dissolved oxygen concentrations on zooplankton emerging from the sediments of two floodplain wetlands in the southern Murray–Darling Basin, Australia. Hypoxic conditions significantly reduced the taxon richness and abundance of zooplankton emerging from the sediments of each wetland, whereas DOC concentration alone had no consistent effects. The effects of hypoxia on zooplankton were partially reversed when oxygen concentrations were returned to normal values within 3 weeks. These findings suggest that hypoxic blackwater events can reduce the availability of food resources to planktivorous biota through their reductions in zooplankton abundance; although these resources may be restored reasonably quickly if oxygenated conditions are returned within a short time.