The increased prevalence of hypoxic blackwater events as a consequence of river regulation and other river management practices poses a threat to the management of many river-floodplain systems. However, we still know little of the effects of hypoxic blackwater events on the aquatic biota. We investigated the impact of hypoxic blackwater events on river-floodplain microinvertebrate and amphibious plant communities by examining the effects of varying carbon (dissolved organic carbon - DOC) and dissolved oxygen (DO) concentrations on microinvertebrates and amphibious plants emerging from the sediments of two floodplain wetlands in the southern Murray-Darling Basin (MDB). Hypoxic conditions significantly reduced the taxon richness and abundance of microinvertebrates emerging from the sediments of each wetland, whereas carbon (i.e. DOC concentration) alone had little influence. The effects of hypoxia on microinvertebrates were partially reversed when oxygen concentration were returned to normal values within three weeks. The results for the  plant communities were less clear because the plants did not grow to an identifiable size during the experiment. Nevertheless, the limited data indicated that hypoxia had no adverse effect on seedling density, and instead, seedling density was significantly higher in the hypoxic treatments for both wetlands. These results suggest that hypoxic blackwater events can severely reduce microinvertebrate abundance in river-floodplain systems, although microinvertebrate abundance may be restored reasonably quickly if oxygen returns within a short time (three weeks). In comparison, the seedling emergence of some amphibious plant taxa may actually be promoted after being exposed to the hypoxic conditions associated with such events.